I deal with lots of shrubs, thorns,
perennial weeds etc. and I always find that if they grow through a raised bed or hugelbed that has been mulched and planted it's pretty obvious. It's like on sesame street; "one of these things is not like the other things..."
Once a large perennial plant pops though, I wait until it's put some
energy into the new shoots and then I go at it with a pair of garden shears.
Also, I'm not being condescending with the sesame street stuff, this is just how my mind works.