Page Layout ⇒ Overlaping page footer and content

[asalas77]

In multiple places in my document I have page content that extends over the bottom line of the footer and overlaps with the text. I also get

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Overfull \vbox ...

in my build output. I more or less get what hat means but how do I fix this? From various stackexchange questions I gathered that this can happen due to code not being hyphenated on right margin, but why on bottom, and even with normal text, not lstlistings? (see images below)

I don't know what part of my code is relevant so let me know if you need to see some and I'll add it.

[asalas77]

I managed to somewhat fix it by adding 0.5cm to

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\setlength{\footskip}{\headsep+\headheight+0.5cm}

but this seems more like a workaround than actual solution.