His tentacle was still there. Point is if ftg was a guarantee kill like many say, Bee should've never had time to react to save his brother, but he did. Which is enough for me to say their are some shinobi who can avoid it.
Do you know what counter means? Go look up the definition is the dictionary because I don't think you have a clue what it means. Tobirama's FTG got counter by Madara because he was able to react, evade and attack Tobirama without being hit. All Bee did was push Ay out of the way and he lost his tentacle because he was fast, but not fast enough. Also we don't know the exact moment Bee brought his tentacle out and launched it at his brother. For all we know, Bee may have been preparing his attack the moment Minato tossed his kunai passed Ay. Since it was off panel we can't say for sure.
And it doesn't matter what Bee did, he was not the target, Ay was. Ay has enhanced reflexes and speed, superior to Bee's and yet he was left only to watch as Minato's kunai was about to slice him. The important factor is that Ay was not able to react, it doesn't matter what someone else does, its all about the targets reaction (the target being Ay). So whatever Bee did wasn't very important.
Bottom line is there is no shinobi other than Madara and his OP abilities that can react to a direct FTG like Madara did. Not even Killer Bee. If Killer Bee was in Ay's shoes then he would have been dead.