by refilled do you mean:
A) bought a new ink cartrige retail packaged and placed it into the printer
B) bought ink vials and a syringe and manually filled/topped off the reservoirs?
if A) maybe there is a sensor malfunctioning on the printer. if B) maybe you did it wrong (or there is a malfunctioning sensor).
also consider that if just one color runs out, the printer will tell you its low/out of ink.
for example a two cartridge four color (black + primaries) printer will tell you its out of colored ink if you use lets say...all the blue ink but have 100% remaining on the others.