Hi. I've noticed a lot, that when landing (mostly the C172) the papi and ils don't agree with each other. Usually the papi tells me I am good, 2 red, 2 white, while the ils tells me I am too low. Is this a normal real life thing because the ils wants you further down the runway, or is it just a bit of a boo-boo in FSX? Thanks.

If you turn on the VISUAL AIDS in FSX for ILS you can have red boxes so many feet/meters apart.  If you fly the approach at the top of the box, the PAPI probably wont line up with your glideslope, where as the bottom might. 

same thing in real world, you might be a hair high on the ILS slope, but still within tollerances and be perfect 2 red 2 white on the Visual.

Speaking a bit from limited experience, back in the day when I used to fly small Cessna 172s out of our local international airport before landing-fees hiked sky high, I used to do a lot of approaches on long runways equipped with both visual lights and ILS. 

As far as I can remember, my glide path and the lights rarely agreed, especially on one 13,000 ft runway.  Then again, I always try to either fly high to touch down near the end of the runway or fly low to take as less runway space as possible (the ole base was at the end of the runway), plus there were land and hold short operations at that airport. 

In any case, I was told once that those lights won't exactly agree to my ideal glide path because of the, ahem, size of my airplane, whereas the runways were more for larger medium sized jets and heavies.  No doubt, those pilots sit a bit higher off the ground.  I guess it kind of depends on where you fly.

These lights and glideslopes are never designed to give the same information anyways.  The lights are there for visual approach purposes.  They won't always match.