I think I have it figured out. It boils down to this: Numerian appears to be the only emperor Malalas knows of from the second half of the 3rd Century, so he makes Numerian the cause of everything.
Malalas makes these claims about Babylas:
he barred an emperor from attending church service
he was executed by an emperor
an emperor went to war with Shapur and was captured at Carrhae
If we go by those facts, he's talking about at least three different emperors, all of whom predate Numerian by quite some time. Carus was born in 224, so it's likely Numerian wasn't born until 242 at the earliest. According to Eusebius, Babylas died in 253. Numerian would have been a young boy at that point.
The emperor who attended church service would have probably been Philip, who ruled from 244-249. Decius (249-251) led persecutions against Christians beginning in 250. Babylas was imprisoned at that point, but if his date of death is correct, he would have died during the reign of Gallus (251-253).
The emperor who was captured at Carrhae is easy. It's Valerian, another big persecutor of Christians. He led a campaign against Shapur in 260, fared badly and was captured either in Edessa or Carrhae.