Typically this is caused by some recursion and can happen when there are several interrelated fields. Field A is changed - trigger and change field B which then changes field A again and make the problem repeat.
What happens is that your condition is true and the pop up occurs but then another rule will fire, update a value, maybe update the trigering field again and generate another pop up.
A couple things you could try.
Create a blank form put a field a rule and a message box and see how many times it pops up. Slowly increase complexity until it occurs.
I like to add expression boxes to debug at these times. So inbetween each action add an expression box that displays the value or maybe a concatenated list of all of your values. This way you can monitor the values and the sequence they fire to see to better understand the triggers and how they are reacting. Also make your message boxes less generic so you can track each one individually.
Have fun