When Jenny does somersaults through the laser beams, the last two beams are level horizontally and the higher beam is lower than her foot so she should have broken it.
The fish aliens are clearly communicating with each other using the bubbles as speech. This "language" should be translated into English for the Tardis travelers, but it isn't.
Right at the start Cline says "Everybody gets processed." Yet the only one who does is The Doctor.
Calling Jenny "The Doctor's Daughter" is not strictly accurate. She was created by taking The Doctor's chromosomal information and remaking it into a different configuration. There was no outside genetic input from anyone else. This would ultimately make her more of his twin sister, not a daughter.
When Martha, supposedly a qualified medical doctor, checks Jenny for vital signs after she has been shot, she searches for a pulse at the neck. The location of her fingertips is on Jenny's larynx, not her carotid artery, so would be useless.
When Donna is describing the date she's worked out in the numbers, she says "it's year, month, day. It's the other way around, like it is in America." But the US uses the format, 'Month, Day, Year', so the date shown on the panels are nothing like the American format.