Water in wells of new replacement windows

We recently replaced all of our windows with vinyl replacements. When it rains, which it doesn't do much here, the rain runs down the outside of the windows and seeps into the wells inside the house where the windows slide when opened. The company who put them in says that is normal. Is it? Should there be some sort of rubber or other seal that allows the windows to slide but keeps the water on the outside of the house? The water evaporates eventually but I worry a little bit about winter when it might freeze and cause some damage.

It is common on sliders, unfortunately. In some cases, poor installation can exacerbate the problem, but typically it's not a huge deal. It's one of the problems with slider windows in general.

This is one reason why the pros here warn homeowners against purchasing hung windows with pocket sills.

Out here we have over 40" of rain and no problems. Normal unless the water does not drain back out thru the system designed into the window. Not normal if it fills up the track and overflows to the inside sill/stool.

Does anyone know of a sliding window that does not use the track system?

As randy mentioned, that is just how sliders are designed.... utoo is also correct though, that you should not have water pooling substantially. I've seen many bone-head installers caulk over the weep-holes giving the water no where to go. A stuck weep cover or other junk accumulated in the passage could effect drainage as well. Generally, you really shouldn't see any water inside the house. A picture would be helpful if you can post one.

The last couple of homes I was at they were installed upside down (picture windows).

I have also seen them capped over as well.

Nothing short of amazing.

I've seen them upside down AND inside out! .... That one was a couple years ago, and the client had them installed by a "guy" from craigslist... The worst part is, this was a pricey home in an upscale suburb of Milwaukee and they paid a premium for this "expert" installation.

So the bottom line is:
Check and make sure the weeps are not obstructed.
It is ok to see water in the tracks.
It is not ok if water back washes over the track to the inside of the house.