Same thing happened to me yesterday. I even have screenshots to prove the glitch.

Was booked LAX-SJD-IAH-MOB in D class.

Changed SJD-IAH-IAH to SJD-LAX. Screen showed no change to outbound.

But when ticket was re-issued, LAX-SJD was rebooked in Y (full Y...no wonder the system wanted an add collect).

Took a call to 1K desk to easily fix it, but my goodness...what a broken system.

WARNING: don't attempt online changes. Just call.