There are two issues happening :
First Issue : Query taking lot of time in deciding which index to use.
Eg: If we run an query X , then it takes a lot of time (more than 5 minutes) )and on checking the log it was using a index Y.
Now if I run the query X with index hint Y, it runs in couple of seconds.
That means the time it was taking is not in query execution but before that. Very strange

Second Issue : In some cases it is not selecting the right index also. If my query is on fields A,B,C and I have indexes A and A_B_C created, then it is choosing the index A instead if A_B_C