It didn't make sense to me either, but the director made some odd choices with camera cuts that made me explicitly think Negan was talking about Eugene. I had forgotten about the other Dr. Carson at Hilltop, though, that does make more sense. Was an odd directing choice, though. Or perhaps Negan was deliberately playing a ruse in order to confuse Eugene.
Either way, killing off one of the two medical professionals in the known world still seems careless, but certainly more in line with Negan's character that he does have a Plan B.