Here's the source straight from Randy's mouth:
http://www.twitlonger.com/show/n_1snvtrt"Last tweet re #Contra headbands, they're based on the original NES 8 bit version from early '88 where in-game both headbands appeared to be red in color.
Konami asked that we keep one headband red and one blue so we obliged
Anyone who wants to change the colors themselves or swap heads or whatever tickles your fancy feel free to do so. Enough said, now play with your toys & have fun. "
The issue is that they could have easily painted the bandanas the correct color to match the pants for each character AND the original Arcade/NES/Famicom artwork, but I think they were too far along in production, so they gave that BS excuse.