Bundler applies bundle discounts by bundle priority, meaning that it first tries to apply a discount from a bundle with the highest priority and so on. If every bundle has a unique combination of products, then you don't even have to bother with priority. However, as soon as you have the same or a similar combination in more than 1 bundle (e.g. Bundle with products A and B and another bundle with products A, B and C), then you have to set the priority of your bundles. If you want to keep using both bundles in this example, then the second bundle (the one with more products) should have a higher priority then the first one.
This way, Bundler first tries to apply the discount from the bundle with higher priority and if it can't apply it (order doesn't have all the required products), then it continues with the next bundle.
We also have a feature, which allows you to bypass this priority and just prioritize bundle discounts based on the bundle widget from which the items were added to the cart. This feature can be turned in Bundler > Settings > Discount modes.