Depends on how exactly you add the input fields; I suspect the name attributes are off; You should use the dev tools to look at the HTML and see if the name values of the dynamic fields are correct. You can also debug $this->request->data at the submission to see if the dynamic fields are in the POST data at all.
In none of that helps, you should post the relevant code in here.
I have found that it is some weird problem I believe is because of putting the form tag between the table tags. Then somehow the newly added rows by jquery seems to not work. Very strange…
When putting the form tags around the table tags, it solved my problem…
“When putting the form tags around the table tags, it solved my problem”
Faced a similar issue. Solved when I placed the form tag around the table tag. Thanks a lot @thomasg.