This is to give a more detailed note on my bug posts.
I noticed that this only happens when I am using the filters on the skill tree.
All the options are selected by default.
I like to have 1 and 3 unchecked. When I raise a skill to level 9 it disappears off the skill tree because it's "trained" even though I have yet to click on the accept button. STO will either crash at this point or when I click on the accept button.
This has happened to me multiple times, but I am still not sure if it happens every time I raise a skill to 9, but seems like that is when it happens.