Checked out the card twice, so the other one counted as check in

What @farahhaifan describes is technically impossible: presenting the card twice to the same validator will result in an error message and not a check in.

So it looks like the card wasn't checked in at the departure station and then checked in at the destination. This may be corrected online via uitcheckgemist.nl or My NS.

That depends on the time between the two taps, after checking out you can check back in within 10 seconds or so.

Blauwnet says 1 minute (e.g. for the train to Germany in Enschede after leaving the Blauwnet gates there).

TS states that he tapped twice upon checking out, not that he walked to the other side of the station in between taps.

At the same validator you cannot check in again after checking out for one minute, at another one this is immediately possible at NS. At the regional operators you'll always have to wait one minute.

It is unlikely indeed, but the time between two taps at the same pole used to be 90 seconds or else an error ‘you are already checked in/out’.

That time has (years ago) been reduced to (give or take) 10 seconds, so you can easily check out-in-out-in-out-in 5 times within one minute, at the same pole! 

Anyway, contact NS Customer Service to have the extra check-in corrected.