First of all, it needs to come out of the cloner. Your water is either:
A) getting old and needs to be replaced with fresh water.
B) water needs to be changed with higher strength nutes because it's larger now.
C) your roots aren't liking the higher temperatures now that uts past the rooting phase and had an entire root zone now that needs to be much cooler. The pump causes heat issues.
D) such a small amount of water being used to just barely submerge the pump is becoming stagnant and the nutrients are getting eaten up way too quick.