Wheaten should be solid yellow, very little exceptions. A small dot on the head is okay. BBR should be light brown with bold, thick brown stripes down the body and down the head and eyes. Getting them mixed up is indeed an issue, but it can be solved. I think the number one thing someone should know in order to solve this is knowing what wheaten SHOULD look like, at least in a female. After that, they realize who's pushing the standard.
Take this female for example. . . She's half Wheaten, half BBR. She's a female with good example on what not to breed if you want true color.
Next up to avoid are Wheatens with too much darkness at the chest, which naturally isn't wanted but also can clue in on some Duckwing/BBR influence.
Males are a little more tricky, but from my experience. . . Stay away from males with straw or yellowish hackle if you want BBR, stay away from too dark of red or too uniform of red if you want Wheaten.
I'm not sure in helping you with Cubalayas, they are indeed a little tricky as other gamefowl can be. As with other breeds in comparison, there's a lot of methods. Me, I just try and balance things out. I keep out any females too dark of chest or too uniform of color, if my male has too much brown in the breast, I breed in a female with very light coloration. The less brown or black on her breast, the more I get rid of the issue in the male.
Oh and another thing - Get rid of any excess white at the base of the male's tail. Not something you want, despite what people often show in their chosen breeding males in some breeds.