Why Select top 5001 or Select top 10001 queries exceed the exectution thershold value?

Query execution time of 108.4 seconds exceeded the threshold of 10 seconds. Thread: 50; Database: CPT_MSCRM; Server: SQLSER01; 
Query: 
update [Appointment] set [UnitofService]=2, [new_Code]='h3h2d4ew-70d7-e511-sae2w-0930320291s02', [new_EnrollmentCode]=
'g9erhbt9-abc9-ef43-8128-005056e09892' where ([Activitycode] = '90cjhbt9-abc9-ef43-8128-005056e09892').

We also get this kind of warning messages for select query which is like 

Select top 10001 or Select top 5001 , in which it says that query execution time is 210 seconds (Most of the times)
which exceeded 10.0 threshold limit.

When I run this Select top statements in SQL server directly it returns only less than 1000 rows based on the current data set
and it returns in like 2 seconds.

Please help to solve this warning messages.

Thanks.