Using BlueMap-1.6.0-forge-1.16.4 on Forge 36.2.0
Also present on BlueMap-1.5.5-forge-1.16.4

I used the wiki page to install the missing textures from mods (i.e putting the mod jar into the resources folder and deleting data folder) but whenever I do that, it completely messes up the textures on the map like all of them are randomized

The weird thing is also that there is sometimes one or two chunks that render correctly.
I don't know if it is a bug in the mod or I am misunderstanding something

This is likely due to your browser caching some old tiles.
Please use the Update Map button in the web-app if you see such textures :)

If you need more help with this, please visit our discord server or subreddit, since GitHub is not a good place for support.