Here's a solution to your problem using dplyr's filter function.
Although you can pass your data frame as the first argument to any dplyr function, I've used its %>% operator, which pipes your data frame to one or more dplyr functions (just filter in this case).
Once you are somewhat familiar with dplyr, the cheat sheet is very handy.
> print(df <- data.frame(sub=rep(1:3, each=4), day=1:4))
sub day
1 1 1
2 1 2
3 1 3
4 1 4
5 2 1
6 2 2
7 2 3
8 2 4
9 3 1
10 3 2
11 3 3
12 3 4
> print(df <- df %>% filter(!((sub==1 & day==2) | (sub==3 & day==4))))
sub day
1 1 1
2 1 3
3 1 4
4 2 1
5 2 2
6 2 3
7 2 4
8 3 1
9 3 2
10 3 3