I am trying to calibrate my narrowband images, and for the first time I am using WBPP
...
am I doing something wrong? Are my dark flats associated with the flats or not?
Maybe OP is happy now they solved the "problem", but note there was no problem in the first place.
First, darks are dark. No light. So a "filter" is irrelevant. This is why I have believed PI just notes "NoFilter" in the Pipeline view of WBPP. This is what it shows in my WBPP stacks too, for ALL my darks, even though the flat darks have a filter noted in the FITS header. It's just not used and not relevant.
Likewise, you don't always need to be exact in matching flat darks, since the exposure time for flats can be relatively short (OP's are especially short). PI/WBPP takes this into account with the "Exposure Tolerance" in the Darks tab, as has been noted in the thread. 2 is the default, which works for common situations.
With 2 as a default, it will group exposures like your 0.21-0.35 sec. This is because there is practically no difference in the signal (noise) level with modern sensors within that range of exposures. So PI/WBPP just groups them all together labeled as the longest duration one.
Mine similarly, I have 0.09-0.4sec flat darks (from my LRGB filters). It just bundles them to 0.4. It works fine.
If you have much longer duration flat darks, e.g. for a narrowband filter (I appreciate this didn't happen for OP with their short durations), then it will split them out and match them to the flats if they are above the tolerance setting. But you don't have to worry about any bundling going on normally.
My longer duration NB filters are not bundled, since their exposures are longer duration than the tolerance (13, 7, 4 secs).