Разные варианты могут быть с разным смыслом.
1. We (have been waiting) a long time for the bus but
it (has not come).
1. We (had been waiting) a long time for the bus but
it (did not come).
2. That's a nice shirt. Where did (you buy) it?
3. She (sees) me but she (does not speak) to me.
3. She (sees) me but she (is not speaking) to me.
3. She (is seeing) me but she (is not speaking) to me.
3. She (is seeing) me but she (does not speak) to me.
4. (Did it rain)
yesterday? No, it was a nice day.
5. That was a stupid thing to do.
Why (did you do) it?