I have the same issues, and I've got 7000 hours. There's about 100 hours or so of 'gray zone' time and I was told that the only time you can actually log on Airline Apps dot Com is time when you are actually PIC. In other words, if you were receiving instruction in an airplane in which are are allowed to fly as PIC, you may not log it as PIC even though the FAA allows you do do so.

Clear? As mud.

I've got the same worries for any future interviews I might get.

When I had this and interviewed at my current job I simply told them about a couple of minor discrepancies (there were some other small oddities because I worked in Europe and there were a couple of minor differences there in how time is logged) in the interview before we got started. It was not a deal breaker.

Just tell them the truth before they ask about it. They will understand. If they don't, you don't want to work there.

Being truthful in an airline interview is probably the single most important thing. Having slight differences in logged time should not be an issue because of the difference between the FAA definition and how it's done on Airline Apps dot Com.

As long as you weren't trying to pad your numbers, which is a capital crime in aviation.... Doesn't sound like that's the issue, so just be honest.