Nintendo:

"There is no design issue with the Joy-Con controllers, and no widespread proactive repair or replacement effort is underway. A manufacturing variation has resulted in wireless interference with a small number of the left Joy-Con. Moving forward this will not be an issue, as the manufacturing variation has been addressed and corrected at the factory level.

We have determined a simple fix can be made to any affected Joy-Con to improve connectivity."

This jibes with something CNET editor Sean Hollister noticed after Nintendo performed a quick fix on his troublesome left Joy-Con. By taking before and after pictures, he observed that the only change made was the addition of a bit of conductive foam, possibly to shield the controller from interference. Also, a new controller purchased from Amazon lacked the modification, but sported a circuit board with a different manufacturing code.

Nintendo also said that there are other reasons Joy-Cons could have connection issues, but given this information, if you're having problems then you should contact the company and get the fix.