Overlapping Proficiencies From Leveling?

In my game I’m a Rogue with the Entertainer background. Leveled up enough to pick a subclass and decided on Mastermind for the teamwork possibilities. The subclass gives Disguise Kit proficiency, something I already had from my background. If I do the level up in Beyond it insists I pick a new tool proficiency for my background. But I’m not making a new character, I’m leveling up an existing one. How should I handle this?

So far I’ve been treating it as a glitch with Beyond (it sees characters as ‘new’ even if they have experience being tallied) and ignoring it’s suggestion as anything from levels prior to the current one are effectively set in stone barring DM caveat. Still, would be nice to have a more concrete way of dealing with this than a hand wave.