These are false DTMF digits, so called "talk-off". Sometime a person's voice is unexpected picked up as a digit, which gets transmitted to the other party, and played back.
If the beep sound is indeed from a false DTMF digit, you can actually ask your friend to press a digit, and listen to it, whether it just sounds like the beep you heard. It can be attenuated (DTMF playback) by changing the setting below:
Physical interface -> phone port -> DTMFPlaybackLevel
Set it lower than -50 dBm, it should be hardly audible.
However, false DTMF digit is usually random, hardly occurs constantly every 3 minutes as you observed.