I would say all new knowledge starts either with
1. a disagreement (where someone thinks of a different answer for a question which already has a common-knowledge answer) or
2. a new question (where someone observes a pattern in nature or ideas and wonders how it can be explained)
3. a new pedagogy; classification scheme, mnemonic; allowing the understanding of an idea or group of ideas much more quickly and/or clearly.
As far as whether there are any prominent examples in physics--well, that's the whole story of physics and the scientific method, isn't it? You come up with hypotheses--either the hypothesis is confirmed or rejected by observations... Presumably the hypotheses that aren't rejected work their way into theories.
BUT, in the case where the alternative hypotheses would make little or no measurable observational differences, such as in the various
interpretations of quantum mechanics, it varies...
(1) Some people might become entrenched with their own hypothesis. And
(2) others might try to completely ignore all interpretations, and just focus on the math.
(3) Others might try to understand and describe all such hypotheses with as much clarity as they can.
I think it's with this third group where new knowledge comes. Some people in Group 1 might be right... But they've taken their guess and are sticking to it, and are not open to other possibilities. Group 2 is probably right, but they aren't going to make any giant steps forward, because they've accepted the premise that "there are no observational difference between the theories" so they won't be looking for them. Group 1 and group 2 are both dogmatic in some way; Group 1 by dogmatically sticking with an interpretation. Group 2 by dogmatically avoiding interpretation.
Group 3 on the other hand will try to keep a list of leading hypotheses; understand the distinctions between them, recognize both their failures (mismatch between apparent reality and model) and their successes (match between apparent reality and model), and be open to other possibilities.