I have two matrices:
mat <- matrix(1:6, 2, 3)
mat2 <- matrix(1:2, 2, 3)
and a parameter
a <- 1
The length of the return is completely decided by length(a == 1). See also the helpfile with ?ifelse. Your code will only return a single value.
ifelse targets vector input / output. Even if you get the length correct, say: ifelse(rep(TRUE, 6), mat, mat2), you get a vector rather than a matrix output. So an outer matrix call to reset dimension is necessary.
Tip 1:
For your example, looks like a simple result <- if (a == 1) mat else mat2 is sufficient. No need to touch ifelse.
Tip 2:
It is not impossible to ask ifelse to return a matrix, but you have to protect it by a list (remember a list is a vector):
ifelse(TRUE, list(mat), list(mat2))
But, this is inconvenient.