Sorry, but PhonerLite dials what the user inserted. If that is text - then that text is used. Are you using some special formatted numbers that contains brackets and so on? Do you have an example?

Are you using a headset that supports HID (signalling hook events)?
In that case multiple applications (Skype and PhonerLite) react on such events from the headset. In your case PhonerLite is minimized and the headsets signaled the off hook event (connect/accept a call). For this special case PhonerLite reads the clipboard and dials that content.
That was requested by some users that copies a number into clipboard and press the hook button on the headset to dial that number. 

To avoid multiple usage of the headset you can select "Default" for input and output sound device in PhonerLite. Then configure your headset in Windows settings as "default communication device". Afterwards PhoneLite uses you headset but don't react on any headset events for button presses and so on.