I am doing codechef Manhattan Rectangle problem and after submitting my solution I got TLE of (-1.0000 sec ??).I have seen this time limit first time.
Can anyone tell me what does that mean?
It is an error from your side of the interaction.
"Then, you should read a line containing a single integer. If this integer is non-negative, it denotes the answer to your query. Otherwise, it means that you exceeded the limit on the number of queries, the coordinates you printed are invalid or some other error occured."
Also make sure to flush your outputs as @taran_1407 has mentioned here.
Hope this helps 
In interactive problems, if something goes wrong, then program may give any verdict if you don’t exit. This is common behaviour in interactive problems. It just means that you are either not reading grader response well or you are not giving output as specified.
To get rid of this, read the statement and interaction carefully. Like in FEB long problem MANRECT, you may forget to read response after you print the answer for a test case. You must read an integer after printing output to a test case, 1 means your answer was correct or negative integer means your answer was wrong. In the case of wrong answer you should terminate the program to get WA verdict. Otherwise you may get any verdict.