Hello,
There are probably 2 possibilities:
1. You have enabled "Dialer Integration" in Zoiper "Config" -> "Advanced ". Check if it is enabled and disable it.
2. Your device offered "Complete action using .... Zoiper" when tapping on the "Dialer"/"Phone" appliction. It will also have a check-mark "Always use this application". This will make Zoiper default application to handle calls from Native Dialer. To clear this, go to Android Settings -> Applications, select Zoiper and "Clear defaults".
Number 1 is less likely to be the cause, but please check it.