In the PvP matches, you experience more of the BO abilities and skills being used against you, but it is very frustrating not knowing what is happening/what happened to your ship. I can't name the abilities in question, because I have no idea what was used against me.
As an example, the "Attack Pattern Alpha" has a very distinctive power-up graphic, and many of the other abilities do as well.
However, there are some abilities that seem to disable manuevering, (not being tractored, that has a good graphic as well), some reset your tray abilities or induce a 'cool down' timer on unused abilities.
Anyway, several of these abilities seem to cause drastic issues to the player's ship, but many times I've actually thought I pulled my keyboard loose or something like that...then realized it was just some effect that had been used against me.
The graphic indicators either aren't very prominent or they are somehow difficult to see; it may be they only appear on the Firing ship, which can be off camera or just not close enough to really see the graphic.
May I suggest that there be a visual cue on the receiving/target ship, or perhaps even a text overlay in one of the HUD boxes that lets us know what is happening.