9th level Armorers are supposed to have 2 prepared 3rd level spells.  We also get hypnotic pattern, lightning bolt that are not supposed to count against the number of artificer spells I prepare. However those two show as "Always Prepared" and all the others are greyed out. The problem persists beyond logging out and back in again.
Does anyone else have this issue?

You get 2x 3rd level spell slots. This has nothing to do with what spells you have prepared, except that you can prepare spells of that level.

Hypnotic Pattern and Lightning Bolt will be prepared and don't count to the number of spells you can prepare.

The number of spells you can prepare is your Intelligence modifier + half your artificer level, rounded down (minimum of one spell). So, let's say you had an Intelligence modifier of +5. At 9th level, you'd prepare 5+4 spells, or 9 spells total, not including those you get as always prepared like Hypnotic Pattern.

So, going from 8th level to 9th level won't increase the number of spells you can prepare, even though you now get 2x 3rd level slots. You'd have to unprepare some lower level spells to now actively prepare some of these 3rd level spells.

Ah, you are a genius. I just assumed I would be able to prepare 2 more spells if I levelled since I am now able to prepare 2 3rd level spells. It helps to RTFM.

Quote from myDisplayName___ >>

It helps to RTFM.

 Words to live by as an artificer. ;)