What 50 rules did they break by making the polyjuice potion?

Although it's not clear what rules Hermione was referring to, we can see what rules they actually broke:

• Entering the restricted section of the Library and, presumably making a potion that the Potions-Master considers too advanced

Snape said it was in a book called Moste Potente Potions and it’s bound to be in the Restricted Section of the library.’

• Lying to a teacher in order to remove said book from the library

‘Er – Professor Lockhart?’ Hermione stammered. ‘I wanted to – to get this book out of the library. Just for background reading.’

• Having boys in the girls' lavatory

Hermione had overridden Ron’s objections by pointing out that it was the last place anyone in their right minds would go, so they were guaranteed some privacy.

• Stealing from Snape's private stash of potion ingredients

‘D’you realise how much we’re going to have to steal, Hermione? Shredded skin of Boomslang, that’s definitely not in the students’ cupboard. What’re we going to do, break into Snape’s private stores? I don’t know if this is a good idea …’

• Leaving a fire unattended (except for a ghost)

‘Well, as the fluxweed has got to be picked at the full moon and the lacewings have got to be stewed for twenty-one days … I’d say it’d be ready in about a month, if we can get all the ingredients.’

• Causing an explosion in the Potions class

Harry ducked swiftly down behind his cauldron, pulled one of Fred’s Filibuster fireworks out of his pocket and gave it a quick prod with his wand. The firework began to fizz and sputter. Knowing he had only seconds, Harry straightened up, took aim, and lobbed it into the air; it landed right on target in Goyle’s cauldron.

• Having a girl in the boy's dormitory

Harry and Ron, the only ones left in their dormitory, were woken very early by Hermione, who burst in, fully dressed and carrying presents for them both. ‘Wake up,’ she said loudly, pulling back the curtains at the window. ‘Hermione – you’re not supposed to be in here,’ said Ron, shielding his eyes against the light.

• Drugging Crabbe and Goyle

‘How thick can you get?’ Ron whispered ecstatically, as Crabbe gleefully pointed out the cakes to Goyle and grabbed them. Grinning stupidly, they stuffed the cakes whole into their large mouths. For a moment, both of them chewed greedily, looks of triumph on their faces. Then, without the smallest change of expression, they both keeled over backwards onto the floor.

• Stealing their shoes

They also stole their shoes, because their own were far too small for Crabbe- and Goyle-sized feet.

• Impersonating Crabbe and Goyle (obviously)

• Stealing clothes

‘Good. And I sneaked these spare robes out of the laundry,’ Hermione said, holding up a small sack. ‘You’ll need bigger sizes once you’re Crabbe and Goyle.’

• Sneaking into another house's common room

‘Oh yeah – pure-blood!’ said Malfoy, not listening, and a stone door concealed in the wall slid open. Malfoy marched through it and Harry and Ron followed him.

My instinct says that doing certain spells without permission, removing dangerous books from the library, impersonating other pupils and sneaking into other houses' common rooms is probably what Hermione is driving it.