You've just discovered the frustration of trying to convert from PDF's. I feel your pain.
First, read the
sticky, especially the section titled "Some of my paragraphs are split into multiple paragraphs".
Short answer: PDF's don't have paragraphs; they have lines of text. The information to know where one paragraph ends and another begins gets lost in the conversion to PDF, so it's not available for Calibre or any other conversion program to make use of. Some PDF's use workarounds to maintain that information (e.g. by putting blank lines between paragraphs) and therefore Calibre is able to guess where to break paragraphs. The one you're working with apparently does not.
Possible solutions include converting and manual cleanup afterward (a lot of work), using Calibre's heuristic processing to try to guess where the line breaks are (good, but not perfect), or trying to obtain the original in a different format, like epub, mobi, or html. If this is possible, I recommend it as the best solution.