Why do I get “number of items to replace is not a multiple of replacement length”

Because the number of items to replace is not a multiple of replacement length. The number of items to replace is the number of rows where is.na(combi$DT) & !is.na(combi$OD) which is less than the number of rows in combi (and thus the length of the replacement).

You should use ifelse:

combi$DT <- ifelse(is.na(combi$DT) & !is.na(combi$OD), combi$OD, combi$DT)

N.B. the & !is.na(combi$OD) is redundant: if both are NA, the replacement will be NA. So you can just use

combi$DT <- ifelse(is.na(combi$DT), combi$OD, combi$DT)

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