Error - 'Transaction Reference must be unique per supplier'

As the error message suggests, the transaction that you are attempting to upload has the same reference as a transaction already in the system. If you amend the reference, you should then be able to upload.
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Please also check your suppliers to see if the transaction has been posted to the account.
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This also might be due to some aspect of the data other than the Transaction Reference being wrong.
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To identify which rows or rows are causing the problem, you can try uploading rows one by one or in small batches of a few rows at a time to narrow down which one or ones might be causing the issue.
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It might also be worth reviewing the list of data from the source sheet to look for any anomalies or variances in the data.
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In particular, if you have the Sub Ledger code included - then ensure all of the Sub Ledger codes are valid ones.