I'm suprised to see that this particular bug has YET to be fixed. I experienced the problem back in August, shared it on Bioware forums (before this Answer HQ became the supposed "solution" for these type of problems), and still nothing. Anways, here was my situation on the PS3, and I hope that enough players will report this problem so that we can find a remedy before Bioware decides to dedicate all their time and energy on ME4:
"I've encountered a similar problem. However, I noticed that it has only hindered me in obtaining the AR Extended Barrel, the Shotgun Spare Ammo and Blade Attachment, and the Pistol High-Caliber Barrel and Scope. Now on my third play-through, these are the only weapon mods that have remained at lvl 2 (I could only buy them); all others are at lvl 5. My Shepard scans the aforementioned mod with his omni-tool, but it doesn't seem to register (the pop up in the corner doesn't appear), nor will it be at the weapon's bench.
I find it odd that this particular bug (for me, at least) only affects these 5 mods. Even more so, however, when I watch my girlfriend play through the game and she picks up each mod with no problem whatsoever. It's maddening!
ALSO, I've tried saving/ reloading before picking up these particular mods with no success. Madness continues..."
I have yet to attempt another ME3 playthrough, as I fear this bug will just agravate me again. So until a solution arises, be it the community here somehow finding a remedy, or bioware finally acknowledging this bug and fixing it, I'll be busy with multiple ME1 and ME2 playthroughs, waiting for the day to transfer my data and enjoy ME3's single player.