Maybe bad connections. Normally in a 4-wire system a constant current is sent through the PT100 via one pair of wires, while the voltage generated over the resistance by that current is measured on the other pair. If one or more of the wires shows a bad contact, you end with a lower measured value.
Sometimes a 2-wire PT100 is connected to a 4-wire system. It means you'll have to connect a current source wire and a measuring wire to each end of the PT100. If one of the connections has a high resistance (bad contact) then this could result in a measured value which is higher than expected.
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