Pretty sure I missed an instruction

So I got my first set of bees last monday (9 days ago). I put them in the hive (langstroff) and put the queen cage in the middle, hanging by a string. I took out the cork in the cage and put all the bees inside (as many as possible. The entrance had a small and a big hole depending on how you turn it and I used the small hole first. I removed the frames and fake comb that came with it and just put the top strips in.

I did not feed it, but my field has a ton of clover. I have it 20 feet from a pond on the east side, with nice tall trees right by the pond. There is a hill coming down to the pond, and I have it at the bottom. So it will get morning sun, but afternoon shade, but wind is not an issue. (guaranteed since we had a wind storm that moved my brooder house (wood) 50' and tore up a hoop house but didn't move the hive at all).

So I go to check the queen. Plenty of activity around the hive. I open up the top and they have run lots of comb THE WRONG WAY! AHHHH! I put the entrance on the east side, so the tops of the frame run east west. They have run their comb North South. Did I miss the instruction that the entrance must be on the North or South? Is there anything I can do now? Or do I let it be? Is this normal or unusual?

I have not been able to remove the queen cage or check for the queen since I did not want to tear apart the comb and wasn't confident I could lift all the frames at once and fix it.

Thoughts?

congratulations to your first hive!
First thing to know - if they build comb like yours - they have a queen. So no worries there!
Next thing to know - bees don't build comb along the compass - they don't even necessarily build in straight lines either. So no instruction missed.
Yet, if you are in the northern hemisphere and have temperate to cool temperate climate, an entrance south'ish might be preferable, because bees like a warm sun bath. Give the bees a nice warm micro climate with wind protection, but no burning heat from direct sun. Next to a hedge, below a deciduous tree, on the edge to the wood would all be perfect.
Bees tend to follow an already existing start of comb. Thats probably the reason, why 'fake' comb works so properly. A line of bees wax on your top strips might coax them into following the straight line. If this is not enough, for your bees, you can go back to your langstroth frames, remove just the (plastics) foundation and replace this with an inch of bees wax foundation at the top of the frame. You should end up with naturally drawn comb with perfectly movable frames (if you need them). If you don't bother, you can of course keep the comb 'the wrong way', especially in the brood box. Have a look at the 'perone hive' and how perone handles 'the bees part' and the 'bee keepers part'. Perhaps you just give your bees a second langstroth box to fill with comb the way they like for the 'bees part' and give them a little more guidance in the 'bee keepers part' what in a langstroth hive would be called 'supers'.

what do you think?

you'll need to take out the queen cage within less than 24 hours after install

in my hives i don't hang the queen...direct release and snag the cage as it still will have the queen pheromones on it and the bees will build comb around it (hanging or sitting)

Wild comb with foundationless frames is not that rare. I always try to have at least one drawn frame in the box (with undrawn foundationless frames). This helps set the pattern and you are less likely to encounter wild comb. If you don't have any drawn frames, one frame of full (or nearly full) foundation can work as well.

Now that you have a bunch of wild comb, I would leave that box be a crazy mess and try to grow the colony into other boxes and phase out that box. Basically, you can add supers as the colony grows and once the brood nest (and queen) is in a box other than the crazy comb - move the crazy comb box above any honey supers and let any brood hatch out and let the bees store honey in it or move honey out of it as is their desire. Hopefully you will be able to remove the empty box early in the spring after you move the crazy comb box to the top. This whole process may take a year or two depending on how quickly the colony expands, etc. You might get lucky and be able to phase out the box in less time - a lot depends on how quickly the brood nest shifts position. Once the box is empty and removed, scrape the frames clean and harvest the wax.

You could perform a cutout and hold the comb in empty frames with large rubber bands around the frame corraling the comb. They will bond the comb to the frame and often chew apart the rubber bands. If they don't cut the bands, you can do so after the comb is bonded to the frames. Doing this can really set back the colony and is a daunting, messy task for a new beekeeper. I would do the less invasive method and try to be patient.

Doesn't sound like I want yo cut it apart. When do I know to add a super under the brood box? How do I get the queen to go in the new box? Or should I put another box next to it? If I put it under, do I put some sort of separater? My kit had some thin board with a hole in it.

Thanks for the help. Right now I'm happy the bees stuck around the box and seem happy so I have officially started beekeeping.

if you don't want to cut, this will take some time. Ardilla Esch already pointed you into the right direction. The fastest version, without cutting comb and without searching for the queen, uses a queen excluder. (ok thats pretty conventional beekeeping)

Basically, you continue with the hive, as if nothing special happened. The moment the hive is strong enough to fill a second brood chamber, you add a second box with some suggestions in it, how you want them to build their comb (on top). (No queen excluder or other separation at that time)
You wait until they raise brood in the new box. At this moment you put a queen excluder between the two boxes. Because the queen usually is close to the youngest brood, she is almost always in the upper box. To make sure, you got her there, check after 4-5 days, if there are eggs and youngest larvae in the upper box. If you are sure, that the queen lays eggs in the new box with proper comb (is this the opposite to wild comb?) switch the boxes, so that the box with the queen is near the entrance hole. (A hive with an encaged queen tends to be upset pretty soon (a few weeks) and even might kill the queen). Keep the queen excluder between the boxes to allow the brood in the box with wild comb to hatch. (Excluding the queen from the box makes sure, she can't lay eggs there any longer). After three weeks all brood from the box with wild comb should be hatched. Now you have a box with wax and honey, but without brood and could use a bee escape to remove the rest of the bees.

I'd check that your hive box is dead level in all directions. This can contribute to cross combing.

M Johnson wrote:Doesn't sound like I want yo cut it apart. When do I know to add a super under the brood box? How do I get the queen to go in the new box? Or should I put another box next to it? If I put it under, do I put some sort of separater? My kit had some thin board with a hole in it.

Thanks for the help. Right now I'm happy the bees stuck around the box and seem happy so I have officially started beekeeping.

Normally you would add a second brood box on top when about 80% of the comb is drawn out. However, since you want to move them out of the messed-up box - you can do it earlier. If given the vertical space, the bees will often draw out the middle few frames of both boxes before filling out the frames to the sides. That is why normally you would force them to fill out most of the box before adding another. Also, giving them more space than they need means they have to maintain the climate of the extra space and protect the space from invaders (wax moths, ants, etc.). Make sure that new box has a frame of drawn comb or foundation so they don't repeat the freeform comb.

The thin board with a hole in it is the inner cover. It should go on top of the uppermost box and under the telescoping cover. If you don't have it under the telescoping cover, the bees will eventually propolize the cover to the box and there is no good way to pry them apart. You can however pry apart the inner cover from the box easily. That is what it is for and you should use it.

Try to find a local beekeeper near you (often there are clubs) - preferably someone who has at least a few years of experience. Shaddow them during their hive inspections and watch how they move, what they look for, etc. That will give you much more confidence. Remember that there are few situations in beekeeping that need immediate action - ask questions of your mentor (or here) if you are unsure what to do.