Marcus Kohm, the author of KOMA-Script (see his initials), utters about this frequently, but unluckily for TeX.SE usually in German.
Also I would prefer to say, some packages are not fully compatible instead of they are incompatible, because in most cases they work partially and often there’s a workaround.
Every package, that makes a redefinition of titling and heading, is potentially not fully compatible. A well-known example is titlesec, where here on TeX.SE we have already a related question: Incompatibilities between KOMA-Script and titlesec.
Also packages with a heavy redefinition of footnote related stuff are potentially not fully compatible. I myself noticed, that footnotebackref only works with an active symbol (the footnote number is not turned into an active link, confer package manual).
By the way: This works fine:
\usepackage[symbol=${}^{\scriptscriptstyle\uparrow}$]{footnotebackref}% needs "hyperref"
The caption package is according to its package documentation not fully compatible. But actually this was quite more serious in older versions both of caption and KOMA-Script (see also comment below of caption author Axel Sommerfeldt).
As scrpage2 is part of KOMA-Script (but is a package and can be used with other classes!):
- Package
xwatermark relies on fancyhdr, so with scrpage2 you will get error messages.
geometryresets the fromtypepagecalculated margins if you don't use the optionpass(forshowframe). – Qrrbrbirlbel Sep 19 '12 at 18:49