This is going to be tricky to explain. I have a set up zombie spawner in main. It is the kind where the zombies spawn into the water and are funneled to a killing stone where I stand and kill them for exp. Now a days we have mob stacking and zombies and baby zombies stack together. When you kill a zombie it can turn into a baby zombie if thats the next one in the stack. If you kill the baby zombie, the stack gets "sucked" into the block behind it, like they are stuck in the block and slowly suffocate and die if I don't break them out. This happens ever time. Zombie stuck in the back wall set up
I've reproduced this many, many, many times. When killing a stacked baby zombie, the mob will glitch into the block if the baby zombie is touching a block when killed. This happens to husks too.
This is likely a spawner setup issue. You'll have to experiment with different setups. In the meantime, I've reported this to the plugin developer.