Allelopathic plants

Not sure this is posted in the right place.
While I don't really think my orchard is a true permaculture, I still plant a lot of miscellaneous plants around my fruit trees and bushes.  I have lots of comfrey, yarrow, wild carrots, other pollinator plants, etc.  I also had a lot of fennel scattered around, I don't really eat that much but it is good for pollinators and I like the smell as I walk by.  I recently learned that fennel is allopathic.  One of my apple trees next to fennel has not grown as well as others but I just assumed the vigor was less, but I wonder if it is due to the fennel.   I ask AI if there are other common plants that are allelopathic  Some, walnuts and sunflowers, I was aware of but AI said Sage, Thyme and oregano are allelopatic.  I have lots of this scattered about, especially thyme, probably 100-150 sq ft. of thyme.  
Are these herbs a problem?  Any other common flowers or herbs I should be worried about?

It may be more difficult to find an answer to your question since most have done allelopathic studies on annual plants and crops and less so on woody perennials.  That said, there may be some studies out there looking at the companion/allelopathic phenomenon between different woody species, but that does not really sound like what you are looking for.  It may be worth looking at the plant family level--if I'm not mistaken, apples for instance are in the Roseaceae (Rose family) and it *may* turn out that some weedy annual and perennial members of the community, in sufficient numbers, might prove inhibitory to apple tree growth and/or production.   If you were to find examples then, in ornamental rose production where this has been observed, it might give some validity to the same effect happening in apples.  But worth noting is the companion side of the equation where some weedy species may, in some way, be beneficial to the tree(s) as understory partners in the orchard.  For example, if one or some of those weedy species harbor microbes or insects that prove also beneficial to the apple trees, then those trees may witness reduced insect predation and microbial disease.  So if you can't find information specifically on your fruit trees or shrubs, you might find some answers regarding other woody species to which they are related and for which deeper analysis on allelopathic and companion interactions have been observed and documented.  Good luck!....

I don't know much about these plants being alleopathic.

They do seem to like different soil conditions to apple trees.  Instead of blaming the plants, listen to what they are telling you about the soil.  Fennel for example, can be a pest in the rigt soil, but I've never had it survive near fruit trees because they have such different soil needs.

I would start with the soil.  How is the ph? The organic matter?  Moisture?  You could do a home pnk test or send out for mineral analysis if you are new to soil.

Fennel being allelopathic is real but it's worth checking what the fennel is actually telling you about that spot first. I had a similar situation — fennel doing well right next to a young apple that wasn't thriving — and it turned out the soil was more compacted and drier there. Once I improved it the apple caught up. Might be a soil signal more than the fennel actively suppressing it.

I think if you've got a good mixture of plants then the benefits will generally outweigh the downsides.
We had a thread recently on Fatalistic Fennel that suggests that the allelopathic effect is mainly in the seed (to inhibit germination). If that is the case there would likely be little effect on established plants and trees, and the beneficial effect from predatory insects attracted by the flowers would fully compensate for that.

One member of the forum grew a plant as an experiment in cedar leaves.

Cedar is alleopathic so I feel that alleopathic might be a real thing or maybe a bunch of hype.

The best way to find out is to do some experiments and find out for yourself.

Look at the other plants/trees around the fennel, are they doing okay or are they stunted?

How is the ph? The organic matter?  Moisture?
pH 6.5, organic matter 4%, moisture and drainage are good.  Two asian pears 20-45' south and another apple tree 20' to the north are all growing much better than the apple next to the fennel.  Pretty much everything I have planted is thriving, including the fennel, except rhubarb and calendula.  The later two do well until summer then they wither away.