That, in particular, would probably need to be resolved by your package use in the preamble for pdflatex, or by using a UTF8-friendly typesetting engine instead, like XeLaTeX (and that is one reason why I prefer it, along with being able to easily use modern system fonts).
So I would try typesetting it with XeLaTeX in the program you typically use for doing so, or if you use the command-line:
latexmk -xelatex compiled_document.tex
It might still fail on the other issue, but if it clears that one, you have a way forward. For package options with pdflatex, again, StackExchange has just about every question asked and answered that I’ve ever searched for. I checked, and it even has specific advice for occasional usage of Greek in a text!
As for the other one, I agree with the above, it’s very hard to say what is going on without an example. I’ve never had problems with sequential footnotes before.