I've noticed this as well.  New capital ships start construction, even while I'm still researching the next level of command

The only time i've ever noticed this is if i have, say, 1 capital point and 57 fleet points left. I then go to research either  more command or fleet points, and then i start to queue up my ships. Now, the first ship starts to build, even though i have more ships queued up after it, so my readout would be let's say -2 capital and -100 or so fleet points. That's because i have enough space to begin with for the first capital, but the other two capitals i queue up wouldn't build after it.

If i canceled construction of the capital and then queued it up again, it wouldn't build because my fleet points were at negative before i began construction.

Is this the case you're talking about?

this isnt a bug, you have always been able to prequeue construction of ships for the incoming supply and/or capital crews.

however the actual construction doesn't begin till the supplies or crews arrive. The idea is that you can queue, while the supplies are being brought up from your planets, and or crews being brought up to your capital vessels.

-AE

You can complete a ship before the research finishes...

I've also found that the Fleet Supply is buggy.

Had some spare supply and queued up some ships over the supply limit, cause I was researching next step. Sent them directly to the enemy planet and they obviously got killed slowly. At some point the whole production queue and supply bugged out and I was listed with -90 supply after having about 100 to spare pre reseasearch. Had to remove the whole queue to get the proper supply back.