I would say that the first thing is to find out is if the difference is precisely the same on every move 0.025mm or if it varies, that is for a 1mm move it is off 0.025mm but for a 10mm move it is off 0.050mm.
Is the error on every axis or only on one axis? Is it the same error on each axis or does the amount vary depending on which axis you measure?
Some "precision" leadscrews are guaranteed to have no more than 0.001" error in 12" (0.03937mm in 304.8mm). Many slightly less precision are rated at 0.003" in 12" (0.118mm in 304.8mm) and others the manufacturers don't even bother to tell you what the error is. So the error could actually be in the leadscrew.
Finally, you are talking about a very small error. It could be in the bearings on your leadscrews, the mounting of the nut or the flex of some part of your machine.