FNEI doesn't seem to function correctly when this mod is being used.
FNEI loads and appears properly, but I can't view the recipes or usage for many of the items, as if they don't exist.

Tried disabling all others mods and only ran FNEI and MSI 2, and the problem persists.

I don know how fnei works. But, maybe it is because I do disable many technologies for my missions

FNEI allows you to view all the recipes of items and what they can be used for. Normally, you can see their recipes and usage even if you don't have the technology unlocked.
Also, when using the command to unlock all technologies, FNEI still doesn't work.
It's not too big of an issue, I suppose, since the game is still playable.

Have you tried turning on Show Hidden Recipes, Show Disabled Recipes, and Show Hidden Items in the FNEI settings?

With those settings on, I have yet to encounter any issues searching for items using FNEI Search instead of Default Search, but you have to keep in mind that FNEI Search searches the internal name and not the displayed/localized name.

I haven't checked. The problem was that I could search for the items and they would show up, but when I clicked on the icon (like, let's say, passive provider chest), it wouldn't do anything.
I've already updated to 1.1. Once MSI2 updates to 1.1 and if FNEI updates to 1.1, I'll have a look.