Sometimes when I try colonise a system with the vodyani the ark does not anchor fully. The button is greyed out and can't unanchor. Tried reloading but doesn't fix.

Screenshots. One system doesn't even have the 4 planets the correct colour.

Try the 1.05 preview branch, it should solve that issue:
https://www.games2gether.com/endless-space-2/forums/65-general/threads/25869-1-0-5-preview-patch-notes?page=1