The timer will pause if you get an incoming phone call. After you take the call, tap the icon on the SE Timer to continue your session.
If you don't want to be disturbed when you are using the SE Timer, you can put your iPhone in "airplane mode" while using the SE Timer so you won't be disturbed by calls and the timer will finish uninterrupted. Of course, you have to remember to take your phone off airplane mode when you are done.