Can't open some PDF files

These are probably very basic questions but here they go. I am having some trouble opening some PDF files from my school's website. I can download them just fine but when I try to open them a window pops up saying the file could not be open because there was an error.
The tricky thing is I was able to download and open PDF files from other sources (mainly email).
Because of that I went into Adobe's website and dowloaded and installed both Adobe Flash and Adobe Reader over the copies that I already had on my computer. Is that bad? Does the computer just write the new copy over the previous one I had without a problem or does it now have duplicated files in the program's folder that could lead to future malfunctioning?
Even tough I haven't noticed any changes in performance yet could that be concern for future problems (crashing, computer slowing down)? Should I reformat the HD to factory settings and start from scratch since I do not have almost any info/ files in the computer yet? Or am I better off  leaving the computer as it is and not messing with trying to reformat.
When a
The other question I have is can there be PDF files that open only in Windows OS and PDF files that would work on both?
Thanks in advance

Probably you're opening pdfs using Preview. Preview is very good and it'll open almost any pdf but not 100% of them, for that you must use Acrobat Reader.
What you did was fine, just keep using the computer.

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