I've given our lemon tree a rather drastic prune (end of winter in Australia), and now it is shooting all along the what is left of the branches and trunk. What should I do please? Oh, it's in a pot and it's first season gave us 16 BEAUTIFUL lemons. :)
You may have over pruned your Lemon Tree.
You should only remove about 1/3 of the branches in any given prune.
It sounds like it is stressed and container planted Lemon Trees will tend to send out sucker shoots. These should be trimmed away right away as they take energy away from the tree.
You will need to give the tree time to recover.
Here are links to refresh you on the care.