The Not So Short Introduction to LaTeX2e (Version 5.03, April 25, 2014)のp.93を参照すると、 pdfLaTeXの説明で、
The bad news is that graphics in Encapsulated PostScript format do not work with pdfLaTeX. If you don’t define a file extension in the \includegraphics command, graphicx will go looking for a suitable file on its own, depending on the setting of the driver option. For pdftex this is formats .png, .pdf, .jpg and .mps (METAPOST)—but not .eps.
The simple way out of this problem is to just convert your EPS files into PDF format using the epstopdf utility found on many systems.
と書かれているので、.epsは全て事前に.pdfに変換しておいた方が無難だと思います。