When only five or six misplaced facelets remain on the cube then it may be a case where only one misplaced facelet can be fixed such as in the following examples. As you can see on the first cube below, the yellow & blue misplaced facelets are in the right locations to match the setup for Sequence 3C-E2 (second cube) but while the yellow one is the correct color the blue one is not (should be red). For that reason only one misplaced facelet will be fixed as a result of doing the sequence. The misplaced facelets that are not part of the setup can be ignored.

On the first cube below, only the blue facelet on the top face matches the setup for Sequence 3C-E4 (second cube) so using it will only fix one facelet as shown.

Another way to fix one facelet on the above configuration is to use Sequence 3C-E2 by first matching the setup (shown on second cube below) with a half-twist of the front face as shown by the first move on the first cube below. After the first move, the red facelet on the front face is the right color but the blue one on the top face is not (should be yellow) so only one facelet is fixed as a result of doing the sequence.