So In Beyond its letting my place a +2 in one ability and +1 in the same ability when your building your character. That contradicts with the rulebook that says it must be different scores. Is that correct?

Definitely don't sound right, I also checked this with the three +1s, same thing, you can place all three into the same attribute.

This has been a thing since Tasha's was introduced. The system is not set up for the option properly to prevent this and it's not worth redoing the entire ability score system to fix when it's a simple case of a DM going "don't do that or I kick you from game", which they would do even if it was pen and paper. And since the rules are right there on the screen when they choose them, nobody can claim "but the system let me and I didn't know".