That is a longstanding issue and it's hard to predict when transitions will work as expected and when they'll interfere with other tracks. I've had the problem show up in just one or two transitions in a huge project while all the other identical transitions worked normally.

If you're having trouble now, the easiest workaround is to use keyframes and run the opacity from 0 at the start of the clip to 100 at whatever point you want the transition period to end. Do the opposite for the fade out and no tracks will interfere with any other.