Alternative = Inaccuracy

I've had this happen several time. I was trying an different ending of how the game could have gone on, so it wasn't "preanalyzed" so I was trying a move Bd6 and it said that it's bad and Bh6 was best. So I went back and moved to Bh8 instead and it said Bh8 is best and Bd6 is an alternative which a second ago was shown to be an inaccuracy

Perhaps it took more time to analyse?

It shouldn't it's all the same settings and all the same moves, basically the game was over with mate on move 22 and I tried out what would happen if mate wasn't hung, so it's the same depth and circumstances for both variations and there shouldn't be such a big difference of 2 pawns

Sometimes it analyzes more deeply; usually when at first it took a short amount of time.

Hmm. Weird. I guess it doesn't find the best move at first sight. I once tried the Stockfish L10 on another chess app and first, it comes up with the first move that pops into it's head but then, it goes to an another move in only 2 or 3 seconds.

I've set the position up from scratch. 2nk1b2/8/1r6/3r3p/P4Q2/5B2/1PP2PPP/5RK1 b - - 0 1

It's not showing it as an inaccuracy anymore, but the difference is still very large and calculation time is out of the question.

Analysis above 10+ is more inaccurate in general. Plus, you are already winning, so who cares  Seriously though, you will get different analysis at different times.