This is common if your taking the boat right out of the water after a run and the engine is up to temp..The reason is the water from the motor runs back out of the engine and back through the pump when you take the boat out of the water.
Otherwise you may have a cavitation issue if the pump was warm with it still in the water....Doubt it though.
On some race boats I have played with we had an overheat issue while idling and the steam used to blow backwards through the pump after pulling it from the river....It is really cool to see steam blowing out of the nozzle....

It just breaks a lot of stuff to do so.

The bowl bearings are completely surrounded by water, so to feel the heat from there, something would have truly had to have gone wrong.....
edit; Willing to bet the pump was hotter on the left side...

GT