Agency recovering hotel costs via Contractor's expenses on timesheet - advice pls.

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Advice please.

The agency paid for my hotel costs as the client refused to pay (long story).

I submitted my chargeable expenses through the portal as usual and the agency has changed the values, basically removing two of the fields and adding a field for 'hotel'. This changes the amount I'm claiming for as two hotel stays are more expensive than what was removed. It works out about another £100 more than the original (authorised) and locked timesheet.

The agency said they are merging the costs together and the amount I claim is the amount I originally put down on the form.

I have to invoice the agency through my umbrella company and I understand the invoice has to match the expenses on the timesheet.

I'm going to speak to the umbrella company - is this normal practice?