Yes, each assertion you receive is separate but if an assertion is made on multiple transactions, you may, but are not required to, resolve each transaction separately. (I use the word assertion to mean a single communication from the consumer which may contain one or more disputed transactions. Two separate communications on the same day would be considered two assertions.)
You will not find a section of the Reg that specifies this because the entire error resolution section (205.11) consistently refers to "notice of error" from the consumer, not "errors". An error is defined in section 205.11.a.
The regulations makes two stipulations for each assertion (205.11.c):
1) You can take up to 10 days to make a determination; and
2) Once you reach a decision, you must communicate that within 3 days.
This means you have up to 13 days, not a blanket 13 days, to make and communicate a decision for each asserted error. For example, if you have two transactions disputed on the same day but resolve one on Day 6 and the other on Day 8, you must send a notice for the first no later than Day 9 and the second Day 11. You cannot wait until Day 11 to communicate both. Remember that you are not required to resolve them separately but if you do, you must communicate them separately. What you have noted in your file or system should be your determining factor because that is what the auditor will use.