I'm DM-ing an upcoming campaign and am considering banning or nerfing spells like Comprehend Languages because they can be used to instantly solve potentially interesting problems like reading an ancient text.

I'd prefer to avoid banning spells and would like some advice on techniques for working around (better yet, working with) these kinds of spells that could make otherwise interesting puzzles and challenges boring.

I've gathered that concealing the information in something other than the literal meaning of words (e.g. ciphers, steganography, Thieves' Cant) would defeat the effect of the spell. This either makes understanding the language essential to solving the problem or it renders the spell utterly useless, so it seems suboptimal to me.

How might I design a puzzle such that Comprehend Languages (or a similar spell such as Tongues) would provide an advantage without outright solving it?

The puzzle that inspired this question was from a D&D podcast where an ancient text was on a pedestal and the text itself basically gave away the solution to the puzzle once translated. The DM forgot that this particular spell existed, so the Wizard used the spell and totally thwarted the puzzle. I'm hoping to be able to create a similar puzzle without either nullifying the spell or requiring its use. I'm not totally sure if I will use this in my campaign, but I want to keep it in my DM toolbox.

Side note: I am working in D&D 5e, though this question could apply to other systems with spells in the same vein.