Two separate breakers for one 240v appliance?
Yes, when you see a janky mess like that, remove it immediately.  Single circuits shouldn't bridge two breakers, with one exception.   

You have to look at the ampere requirements for both the microwave and the heater.  Heaters need circuit breaker capacity of 125% of the heater's requirement.  If that is within the circuit breaker's rating, it may be appropriate to have both on the same breaker. 

A 240V-only load needs either a 2-pole breaker, or two adjacent, matching breakers which are tied with a listed handle tie.