If you've got good infiltration, this isn't a problem—it is something to be happy about. The purpose of a
swale, first and foremost, is to slow, spread and sink
water into your soil. If rain water is sinking in before it even gets to the swale, that's fantastic. In the end, you are capturing that moisture and putting into the soil.
Are you seeing any evidence of run-off elsewhere? If not, don't worry. Yours may be a "100 year swale", built to capture that rare heavy rain event where the ground becomes so saturated that water runs down and fills your swale.
Perhaps the only way you'll really know what is going on is to stand out on your field the next time there is a big rain storm and actually watch to see if water is, in fact, running down into your swale. I would imagine that some is, but that it is quickly wicked into the ground.
Just out of curiosity, do you have sandy soil?