Hi Senem
Kindly help me with the following questions to isolate the issue :
How many users are not able to access CRM even after clicking on Yes or is it just one user?
What is the Update rollup installed on CRM server?
What is the exact error message in User Interface?
Does IE hangs after clicking on Yes and you have to forcible close it from the task manager?
Does this issue happens in IE 9 browser, you can also check by clicking F12 from you keyboard and select IE 9 and try?
Also go to Tools in IE 10 > Compatibility View Settings > Enable the option "Display all websites in compatibility view" > close and then try to access CRM for the affected users to check if the same issue occurs again.
Thanks