I'm still playing my huge game (14-15 hrs in, just starting to take out other civs) and I see the same - armies of 2-4 pioneers wandering around.  Not necessarily stuck but wandering through my territory - even though I've essentially claimed a corner of the map and have nothing behind me.

I'm also seeing stacks of 10-20 enemy armies just sitting there - I just declared war on Altar, who had a stack of 17 armies sitting on our border.  I guess its better than trying to chase them all down...  he's only got 2 cities, so I'm just going to contain and try to take the last city.  

17...

Maybe the AI knows that monsters aren't likely to hit their newly founded cities or pioneers?

https://www.dropbox.com/sh/igu3c3j502u80zt/bi5rguJtEP

to a save game, with the 17 (seventeen!) stack of altar armies that had recently split up.