Certain online submission services check the fonts used in the submitted PDF file. Many of them allow only Type 1 and TrueType fonts in the PDF. Type 3 fonts which may not scale well in printing are not allowed. I got the error shown in the screenshot above when I tried submitting to one such website.
Find out which fonts are being used in your PDF and for what objects. This can be done by using the PDFFonts tool as described here. For example, I found that I had been using Type 3 fonts in a SVG image and in a plot generated by Matplotlib.
Next fix the source of these font problems. I edited the SVG image to use Type 1 or TrueType fonts. I requested Matplotlib to use LaTeX fonts for text rendering, as described here.
The PDF file regenerated from these files passed the font checks 😊
Tried with: Ubuntu 14.04