No, the internal rhyme of a line is very important, but it does not affect the rhyme scheme. Rhyme scheme is just a way of representing the pattern of end rhyme in a poem through the use of letters. For example:
Mary had a little lamb (A)
Whose fleece was white as snow (B)
Everywhere that Mary went (C)
The lamb was sure to go (B)
Because "snow" and "go" rhyme, they are assigned the same letter. If a poem like this had some internal rhyme (rhyme within the line), then it would change the sound play of the poem, but the end rhyme would remain the same.
Internal rhyme does not affect the rhyming scheme of a poem. One can identify internal rhyming, and also identify and know the rhyming scheme of a poem(end rhyme). So this two do not touch each other.