Yes, it was there. Polar Lights faithfully includes in in there 1/350 model kit, researched by Gary Kerr. What it is, is up for grabs. Some think the intent was that it be the phaser turret.
I just checked, and the "tallywhacker" is definitely there on the Art Asylum model too.
It seems to be transparent on the AA model. I never noticed it before either, but it must always have been there. I think it just stands out a bit more in the screencap posted in the OP because it's colored red.
Maybe it's a sticky space lolly pop got stuck on the dome.
That's probably what happened.
Captain Robert April had a sweet tooth.