Hello,
This is an issue that has been occurring to me since the launch of 3.3. I play on PC in Borderless Windowed mode. I believe there is nothing wrong with the client itself, but rather with how the hot bars are programmed. Something seems to have been changed with the recent adjustments to the UI.
I believe this problem may occur in other situations, but here is an example in which it occurs:
Zone: The Fist of the Father (Savage) ... (I believe it may also occur in normal mode as well other vehicle fights, but I have not tried anything else.)
Time: June 7, 2016 (Approximately 18:00 PDT)
During two points in the fight, the player is required to gain the bird buff to avoid the damage from 'Boost'. During this time, the main hotbar (represented by a "1") is replaced with the vehicle bar. Button 1 allows you to attack while Button 2 allows you to 'dismount' (or turn back into your humanoid form). Once you 'dismount', your main hotbar should return. This is how it was worked in the past, prior to patch 3.3. Starting tonight, the hotbar has been replaced with the Pet Bar (to command Egis and Fairies, represented by a "+"). Thus, I was forced to manually switch back to the main hotbar when it should have been automatic.
Note: I play summoner, so I believe this error may be linked specifically to people playing on pet classes. I asked the scholar in my group if she was encountering the same issue, and she was. Myself and the scholar have been clearing this fight for many, many months. This is the first time it has ever happened to us, leading me to believe it was caused by something that was changed with the 3.3 patch.
Please let me know if you need any extra info. I did not get any screenshots of the occurrence because I was concentrating on raiding, but I could probably make some replica screenshots to explain what is happening.