I'll risk a theory...
-- Even in DA, this is something i see often. As soon as i conquer an AI planet, the PIs listing & queues get confused. Their previous ongoing projects are simply left in pending status until i either let them complete or change it for buildings of my own. Strangely, a capital or super-project started by them stays up on the local lists for later use after i delete it from the surface or if it completes on a planet of my own! You may say, gee we can have two or more Economic Capitals. Not so, as soon as one of them finishes, all others disappears.
-- AFAIC, this isn't a bug either since your own race settings take over and the PIs you just conquered or flipped are simply resetting to your currently available (because, in fact, AIs can lag or be ahead of you in research at the time, thus the *no-match* trigger) PI values & names.
-- TA is the same, except 12 different techtrees take over as does their highly variable PIs. In which case the reasoning above still applies.