Not easy to tell just looking at pictures but I get the feeling that red connector's brass contacts are just not up to the task. Either they are getting spread and then loose fitting to the solid pins or the red shell is not going fully into the socket - so they aren't fully engaged. Could be those contacts have a design or material defect so they are not gripping as tight as they are supposed to. Given both times you've seen the same thing, in my case I'd probably go with what you tried before - run bypass wires down a spare tube or make an opening for wires, and bypass that fried connector pair with good connections you can trust.

If the pump was stalling at power up it would draw a lot of extra current but with 20amp fusing, it should pop the fuse, not just cook the connector. About the only way to "test" the pump for stall or overcurrent when running is get a DC ammeter in the circuit and see what it does at each pump start and then running. Try it a bunch of times. Also verify the fuse itself really is a 20A fuse, just in case it is running way overcurrent but the fuse is not a 20...