I think it goes something like this:
At puberty, girls grow breasts, which changes their shape and their balance and their muscle/soft tissue ratios, and so their throwing style changes. They need to re-learn how to throw well with their 'new' bodies.
We have a culture where gender stereotyping is rife, and adults say things like "Don't throw like a girl", giving girls the clear message that they throw differently from boys, and badly. So girls expect to throw differently and badly.
However, the gender stereotyping starts (long) before puberty, so girls begin to expect to throw differently and badly years before there is any real reason why they might.
It becomes a bit of a self-fulfilling prophecy, and (many) PE teachers and others don't bother to teach girls how to throw well, because the gender stereotyping in their heads tells them girls throw badly anyway - it's just 'natural'.
We don't know what was going on inside the head of this particular PE teacher when he told this group of girls "Don't throw like girls". Maybe he intended to challenge them to throw better, but the effect will have been to reinforce the stereotype.