Quoting DarkSide73, reply 23... so the problem was introduced with the Advent.
Nope, it was happening in the v0.6x TEC only versions, still happens in v0.76.
FWIW: in my current game (huge, multiple star map) it seems that mainly Solanus Adjudicators fall victim to this problem.
Edit: I'm not sure if it was related, but earlier on in this game a small group (IIRC 4 of each) of disciple & defence vessels were attempting to leave a grav well without going through the phase lane.
They got about 5-10% outside of the outer ring of the well before I noticed them.
I was able to order them back inside the well and then send them onto another planet.
Interesting - that you saw it prior,I guess i Lucked out because it was not happening on my prior build