By default, when you are on a call in Lync, and you get a second incoming call, you will get both a toast and a beep sound played to alert you to the second incoming call. If you wish to disable this, please follow these instructions:
1) Navigate to "Ringtones and Sounds" in the Skype for Business client.
2) Click "Sound Settings" towards the bottom right.
3) Then scroll in the "Program Events" section to "Skype for Business" and "Second incoming call". Here you can choose another sound or disable completely, select "None".