There is no rule against having multiple breakers in the same circuit. The drawbacks are only the wasted money and more things to troubleshoot when something goes awry, i.e. the well pump stops working and now you have 3 breakers to check instead of one. But you have a slightly different situation after you posted this:
... but I did tell the electrician to wire me in a 120 plug [the] for a
small electric heater ...
What that did was change up the definition of your circuit from being a "branch" to being a "feeder". A branch circuit is one that is the LAST circuit before the load. If you had ONLY the well pump at the very end, then the one breaker in the panel at the house was the only one necessary. The one out near the pump could have been a non-fused disconnect switch within sight of the well. The same could have been true of the "Reliance" box circuit as well (although most likely they only come with breakers).
But by having the electrician add the 110V circuit at the well head, you now have TWO load circuits, so you need TWO branch protective devices there, and the breaker in your house panel is now the feeder for those branches. It's not a problem regarding the size, either way they are just protecting the conductors so as long as your feeder conductors are at least #10 you are fine, as well as your branch conductors for the pump itself. But now your 110V circuit must have another branch protective device. Assuming there was a good reason for the transformer (i.e. no neutral conductor run out to the well), you must have some sort of branch protective device for the primary of that transformer at the very least. Hopefully there is. Could be fuses, could be another smaller 2 pole breaker, but there must be something there protecting that transformer.