It's not broken. It has been changed with TU8 (just wasn't mentioned by the devs at any point).
The total of your mod inventory now includes all gear mods and skill mods that you have applied to your gear and skills.
Prior to TU8 applied mods did not count towards your inventory total.
If you make a count of your gear and skills you will find you have 58 mods applied to your items (gear and skill mods).
This leaves you room to hold only 42 spare mods.
Kap.