Ive noticed one thing VERY similar to this. May be the same thing - I dont know tbh.

I had a unit milling around the base of a seige tower refusing to climb inside. I had a good look around and notice 2 of the soldiers from that unit had been pushed magically through the wall at the base onto the city side base of the wall.

Hence the Unit of soldiers kept trying to reform, but where unble to do so because I hadnt bashed the gate in yet. Thus the 2 soldirs on the inside hadnt been able to magic themselves back through the wall into formation.

I had to leave that unit, but in another battle I saw it happening again so I blew the wall open and ordered the unit to run to the hole in the wall. Sure enough the magic soldiers were reunited with the formation - just for testing I then ordered them to climb the siege towere - which they did.

Houdini soldiers !