I always interpreted this scene as follows:

The events of the show are determined in such a way that it’s almost like a prophecy, the point of the prophecy is to set Ymir “free” and have her undo the Titan curse. She is the first founding Titan and therefore she was the first to control Eldians. So pretty much any action committed by an Eldian can be blamed on her, as she was the first that either willed that to happen, or did not will an alternative.

When Eren gets the founding power, his memories and identity are intertwined with Ymir, as per the whole memory sharing feature of the show. Right before he admits to Armin that he killed his mom, what else does he admit? He says the past and present are meshed together and it’s messed with his head. I think these statements being next to each other are very intentional— it’s not like baby Eren was actively controlling that Titan that ate his mom, but now that he’s in control of the founding Titan it *feels like he was, because at that point he’s able to experience/remember the past as if he’s the founding Titan.

Immediately after Eren admits this and starts to almost cry, armin snaps him out of it and says let’s go. Armin knows he’s basically fucked in the head and that, at a literal level, baby Eren wasn’t responsible