I'm just encountering a problem when I try to intersect two different shapefile: these are all new shapefiles, I made them to descibe the land cover and the land use of a city. The problem occur when I intersect them to create a new single shapefile, in wich the original areas where divided and bring information of both land use, that I have to use for the corine legend: when I use the intersect tool,it create a new shapefile, but just rejected some areas that were in both file and must have an intersection. I tried to obtain them froma a difference between this new intersect shapefile and one of the orginila, but even in this way qgis only recognized some polygon and rejected the others; if I repeat this procedure I can improve the output, but I'm not able to include some areas. The file have the same kind of geographical reference and the same dimension. I also don't understand why the output does change if I use a shapefile first or the other when I tell it wich file intersect. the intersection should not be the same? The images of the files are post belove: the first two are the input shapefiles and the last is the output, it's clear that there are some missing areas, like the big wooded area lower right. Thanls in advance for helping me.

I'm encountering a problem when I try to intersect two different shapefiles. They are all new shapefiles I created to descibe the land cover and the land use of a city. The problem occurs when I intersect them to create a new single shapefile in which the original areas are divided and have information of both land uses, that I have to use for the CORINE legend.

When I use the intersect tool, it create a new shapefile but left out some areas that were in both files and must have an intersection. I tried to obtain the missing shapes from a difference between this new intersect shapefile and one of the orginals, but even in this way qgis only recognized some polygons and rejected the others. If I repeat this procedure I can improve the output, but I'm not able to include some areas. 

The file have the same kind of geographical reference and the same dimension. I also don't understand why the output changes if I use one shapefile first or the other when I tell it which file to intersect. The intersection should be the same?

The images of the files are posted below: the first two are the input shapefiles and the last is the output. It's clear that there are some missing areas, like the big wooded area lower right.

After running a geometry validator: