In order to provide a better understanding of the problem I produced the image below.

The same issue also occurs if I use the “splitter” tool from https://wiki.openstreetmap.org/wiki/Mkgmap/help/splitter

EDIT: The rectangle indicates the bounding box passed to the programs. As you can see in the lower left corner the green are (landuse forest) is not correct because ways lying outside the bounding box are not present although they are part of a relation which is partly inside the bounding box.

SOLUTION:
EDIT: The tool osmosis is able to apply boundaries and keep dependencies intact. It’s a little bit slower but can export multiple files / apply different boundaries in one go without much increased processing time.