I'm doing the Pinching the Pupa quest, already solved the murder mystery quest. 

I fast travelled to the mantisaur nest, the first set of flying enemies when entering the nest I was going to stealth, I'm using a heavy weapon (hammer). 

When I try to stealth it gives me two options X to stealth and Y to hack, when I push or hold X it attempts a stealth while also putting away the weapon, it doesn't put away the hammer and now I cannot attack at all or switch weapons.

Reproduced this issue 3 times.

This happens a lot with the melee weapons it seems. I have had to reload a lot of saves due to the melee buttons not working as soon as a battle starts