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You have a PDF figure, which you want to use in your PDFLaTeX document. When you compile the document, PDFTeX complains about “missing glyphs”, and some (or all) of the labelling text or symbols in the original figure is no longer visible.

What has happened is:

1. Your figure file (say fig.pdf) has a font font.pfb embedded in it.
2. PDFTeX notes that it has font.pfb on disc, and loads that in place of the copy in fig.pdf.
3. It turns out that the copy in fig.pdf has glyphs that aren’t in font.pfb on disc, so that you get errors while compiling and you see that characters are missing when you view the output. (PDFTeX can’t know that the fonts are different, since they have the same name.)

Which is all very undesirable.

PDFTeX does this to keep file sizes down: suppose you have a document that loads figures fig1.pdf and fig2.pdf; both of those use font font.pfb. If PDFTeX takes no action, there will be two copies of font.pfb in the output. (If your document also uses the font, there could be three copies.)

A real case is the URW font NimbusRomNo9L-Regu (a clone of Times Roman), which is available in a version with Cyrillic letters, while the version in TeX distributions doesn’t have those letters. Both versions, as distributed, have the same name.

The simple (“quick and dirty”) solution is to add the command

\pdfinclusioncopyfonts=1

to the preamble of your document.

The “real” solution is that one or other font should be renamed. In either case, this would require that you reconfigure some program’s (TeX’s or your drawing package’s) font tables — inevitably a tiresome job.