Were these stolen items use by a dismissed companion/henchmen? There is a known issue, recently fixed, with equipping armour owned by a previous party member. I don't know if that can be triggered with stolen items, but if you recruit Bairdotr, for example, remove her armour, dismiss her, transfer the armour to another companion/henchman and then back to a main character, that can trigger a reaction to stealing.
The issue in the Equipment window after asking a companion/henchmen to rejoin will be fixed in the next update (no ETA yet). Loading a save in the homestead before asking a character to rejoin will avoids this problem.
