Sounds like growth coming from the root stock. Virtually all named forms are grafted and grafted onto straight Acre palmatum root stock. It is not uncommon for the root stock to produce shoots. These should be rubbed off (or pruned) when you see them, as the more vigorous undergrowth can take over and overwhelm the grafted portion.

btw, there is no "rule" saying you can't prune JM's. Many will benefit from a canopy thinning from time to time and the removal of awkward or congested branching. And you can always (and should) prune out dead wood. It is just that any pruning should be addressed with a light hand and with a great deal of skill to enhance the habit, not alter it :-)

Thank you for your advice!