Double check over your wiring to be sure that you have no shorts and that all connections are good. Loose connections/grounds can cause resistance issues that are easily fixed. Make sure none of the wire insulation is broken and exposed wires are not touching metal.
I'm not 100% sure on a relay causing a blown fuse, but if a pump is going bad it can depending on how it's going bad. If there's a short in the pump or it's not able to spin freely (causing excessive current draw) then those can cause a fuse to blow. I would first check resistance of the relays using an Ohm meter and then do the same to the pumps, or check to see how much current the pumps are drawing while running.