Yes, this is something that you should worry about. Check the length of your objects with nrow(). R can auto-replicate objects so that they’re the same length if they differ, which means you might be performing operations on mismatched data.
In this case you have an obvious flaw in that your subtracting aggregated data from raw data. These will definitely be of different lengths. I suggest that you merge them as time series (using the dates), then locf(), then do your subtraction. Otherwise merge them by truncating the original dates to the same interval as the aggregated series. Just be very careful that you don’t drop observations.
Lastly, as some general advice as you get started: look at the result of your computations to see if they make sense. You might even pull them into a spreadsheet and replicate the results.