It did seem like the umpires were confused as well for some reason. It was pretty obvious that the runner had crossed the plate first, anybody who knows what's going on should have been looking out for that. I don't know what motion the home plate umpire made, I didn't see a replay that showed any motion, but you also can't assume based on no motion at all.
But it also didn't seem like any Blue Jays player was in any way aware of the situation so it seemed like they were all running off the field anyhow. I don't think any of them were even looking to the umpire.
Either way there is no reason for that kind of delay. They ran off the field and didn't appeal, whatever the umpire did or didn't do they would have established that in a matter of seconds and made a decision on that.