Hi questionmaker. I have a few questions for you that might help to find the cause of the issue.
First, are you using true bypass mode or buffered bypass mode? With the Manta's Universal Bypass feature, you can switch between true bypass or buffered bypass by holding down one of the switches while powering up the pedal. Just check the Manta's user manual for details on how to do this.
True bypass uses a mechanical switch (in the form of a relay) which actually opens and closes a metal arm that goes between two contacts. Because the switch is mechanical, it suffers from something called "contact bounce" or "switch bounce" when the arm hits the contacts, and this can cause clicking sounds. This is true of any true bypass pedal, and it's one of the downsides of using true bypass. The buffered bypass mode, however, uses analog switch circuits which do the switching electrically instead of mechanically, eliminating the switch bounce issue.
So, a good first step might be to try using buffered bypass mode.
Even in buffered bypass mode, clicks can occur due to something called a DC offset. Inside the Manta, we make sure that the audio signal is ground centered (a.k.a. AC coupled) by using a suitably large AC-coupling capacitor and a pull-down resistor to provide the ground reference. However, it's possible that the next device in your signal chain (another effects pedal or perhaps the input to the amp) might be "pulling" the audio line up or down if it is not properly AC coupled. This introduces what is called a DC offset, and having a DC offset between two items in your signal chain will usually create a click or pop sound when the effect is switched on or off.
A good way to troubleshoot this is to replace the Manta with another effects pedal and see if the clicks remain. If so, then the problem lies somewhere else in the signal chain.
Please let me know what you think. Also, if you can make an audio or video recording of the click sounds, that would be helpful for figuring out what might be wrong. Thanks!