If you put a filter behind the lens, it will change the focus a bit as the converging light rays are refracted as they pass through the filter. (I think it shifts the focal position by about 1/3 the thickness of the filter glass) - This is why many lenses (especially Manual focus ones) that use rear filters usually have a clear filter installed for normal use, to keep the focus in sync with the marked focusing ranges.

This is also why DSLRs modified for astrophotography (by removing the standard infra-red blocking filter, which also blocks a lot of hydrogen-alpha light (the red colour in emission nebulae), usually replace it with a clear or different IR filter rather than just removing the original - if you just remove the original, then because the filter on the sensor is no longer there, the effective focal distance to the sensor changes and no longer matches the separate AF sensor(s) which are set up to match the main sensor + filter combination.

With an AF camera, adding a rear filter affects both the main and AF sensors - so as long as it can still reach focus, you're probably OK - the camera may think the subject distance is different, but that shouldn't normally be a problem.

I have a vague memory that some rear filter lenses didn't come with a clear filter for normal use, but were intended for use with thin gelatine(?) filters - presumably since they're a lot thinner than typical glass ones, the shift is a lot less.