Problem in pdfs with multi-layer images

I’ve hand drawn some pictures for my thesis using an ipad app called Concepts. The app can export an SVG file, which I edited in inkscape, adding letters and math symbols. From Inkscape I exported the images as .pdf_tex files.

When compiling the whole pdf it gives me the following warning and the pictures are visualised badly in some pdf viewer (such as apple preview). They are visualised correctly in others (such as adobe reader).

PDF inclusion: multiple pdfs with page group included in a single page>] (./cap.pdf_tex <cap.pdf, id=850, page=1, 191.45259pt x 90.78192pt>File: cap.pdf Graphic file (type pdf)

This is how the pictures are visualised in preview

This is how they should be visualised

I partially solved the problem by converting the pdf to ps and then to pdf again. The problem is that the pdf size increases and the quality decreases. Is there any other solution to this problem.