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She did not park the scooter in a place where Lime could access it.
Ms Whitehouse, now recovering in Dunedin Hospital, told the Otago Daily Times on Thursday she had had no contact from Lime, apart from receiving a $39.10 bill for her ride.
''I'm reaching out to let you know that a penalty in the amount of $100 will be applied to your account for misuse of scooter 849599,'' Lime wrote.
''Our records indicate that you were the last known user and our operations team is not able to recover the item because it has not been released to the public right of way.''
Ms Whitehouse was stunned by the email, considering she had an obvious and reasonable explanation for not parking the scooter on the footpath.
''I was hit by a truck and have been in the ICU and surgical wards of the hospital since that night,'' she wrote to Lime.
''The scooter, I am told, was impounded until the police decide what to do with it.
''You can't possibly charge me any extra.''
University of Otago contract law lecturer Simon Connell said he hoped Lime decided not to pursue the penalty notice.
''It's not clear to me that they could legally enforce a charge for not returning the scooter,'' Dr Connell said.
''Lime's terms of service effectively require the user to comply with relevant laws, which could include co-operating with the police and allowing them to take the scooter.''
A Lime spokeswoman said it was ''regrettable'' Ms Whitehouse had got the penalty notice. She said the company would make a further statement, but none had been received by late last night.
Ms Whitehouse's life hung in the balance after her scooter and a truck collided in the early hours of January 18.
The University of Otago masters student has at least one more operation, to reattach part of her shattered skull, but has otherwise recovered remarkably well.
Meanwhile, university vice-chancellor Professor Harlene Hayne said yesterday that helmets would be made available to students and staff using Lime scooters.
Helmets would be available from a range of locations across campus, including residential colleges.
Prof Hayne said the Dunedin campus was considered a pedestrian precinct and users of e-scooters, skateboards and bikes were expected to dismount and walk.
For everyone's safety, scooters would be locked out between midnight and 5am every night, she said.