I can't speak for the app on Android devices, but I have been using it on my iPhone 6s, and I haven't noticed any issues with the timing. I have been using an analogue watch to pace myself, and each section seems to end exactly when expected.
Hmm, I don't have an android to test this with at the moment but I'm planning on grabbing one sometime after Christmas. Are you sure you don't have the time adjusted at all? If you can grab a screenshot it would help me out when I can take a look on the android app.
I used the Android app a good amount over the past few months and have not had this specific problem. Sometimes the app would start a section and then immediately end it (playing the "put your pencils down..." part immediately after "begin"), but that was easy enough to fix (I just pressed the button to start the section again).
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I also just experienced this problem - I know this is an old conversation, but I'm just putting this here for the sake of others who are looking.