I don't think they can scan if you have stolen goods from other base tho.... I just arrive to this new one, and went afk... so I can tell that I am clean.
Beside, even if I have stolen goods on me, and npc scam me, it still seems that I am clean to them, unless I took the goods infront of them...
There is a bug
apparently definitely that sometimes you leave your ship/SRV and the code decides that you need 2 e-breaches, which are illegal.
Since patch 6 I've had this happen twice - and each time, even if you put the items back, next time you get into/out of your ship/SRV, they're there again. I think in your case it was either that or no oxygen as
@Factabulous said. For myself, luckily I noticed and managed to complete the mission without any imperial entanglements.
As
@Episparh says, best way is to check your game log files.
I try not to do AFK in Odyssey unless I can get back to my ship/SRV, and even then try and get away from two-leggeds (trouble makers). Not since last time I was doing a scavenger elimination mission - wife asked me to peel some vegetables that I did in about 2 minutes; got back, despite being on a roof they'd fragged me. One of those situations that it was completely my fault but I still blamed my wife (didn't tell here that though

)