My question is, what are your experienced nurses (especially the charge nurse) doing about this? Having to dump a pt's blood frequently because of a clotted system is obviously not a good thing.
As pp have said, if you can't use heparin (which we often don't in my inpatient setting, for instance for post-op pts), you should flush the system with NS on a regular basis - q 30-60 min, 100 cc - which will be added to the UF goal. Also, observe the system for clotting, if detected early enough most of the blood can probably rinsed back.
Citrate is used in blood banks, it can have effects on CA++, that's probably why it's not an anticoagulant of choice in HD (also more expensive).
Let us know what happens with this pt!