I don't recirculate my paste, yet I find beads in my pumps. Simple things first. Watch for stray bouncing beads if you have an open mill. Clean out your premix cans carefully, and check them for beads before using. Most beads in pumps get there by backing up the feed line to the mill, however, and some means must be provided to absolutely eliminate this source.
Beads can easily siphon back from the mill.
If the change can is empty, and the mill is full of paste or solvent, as soon as the mill is turned off the fluid will rush back down the line. The pump will hold it back only to a limited extent, for a rotary pump is not a tight shutoff, especially against solvent. Don't count on a check valve to hold it, for there is no check valve made to seat against junk, and there is always some foreign material in premixes. Don't count on a siphon loop. Such a loop would have to go up through the next floor to be high enough.