No PDF app showing equations properly
Though Adobe Acrobat (and Adobe Reader) is the official standard tool for displaying PDFs, there are a variety of third-party tools that could have been used to create a given PDF. Though the output from such third-party tools can be passable, the underlying construction of the page layout can vary wildly.

Using Adobe Acrobat, it is possible to use [Cmd + d] to view the document properties, including what tool was used to generate the PDF. I'm not certain if Adobe Reader has the same functionality.