Excel plotting data against row numbers rather than x values in scatter plot

Difficult to debug from a text description. A sample file would be more helpful. That said, the first thing I would be looking at is the nature of the CO2 data's x values. If there is a text string (including empty string or a number stored as text) anywhere in the CO2 data's x values, Excel will not use the numeric values, but will use count/row numbers like you are seeing. Check for text values in the x values and correct, if you find any.

disclaimer: I'm opening in LO calc on this computer, since I don't have Excel here, and LO calc handles these things differently (in fact, LO calc seems to have no trouble with this issue -- are you required to use Excel for this class, or would you be allowed to use a different spreadsheet app?).

Assuming LO calc has interpreted your file correctly, I notice that the first series is using rows 2:196 for the data series -- only including the first text row as the "series name" parameter. Series 2 is defined using full column references, so it is including row 1 in the actual data. As noted, LO calc that I am using here simply ignores the text, but Excel will see the text in the first row and decide not to use the values in column G for the x values.

Fixing this in Excel should be as simple as editing the 2nd "CO2" data series so the data series y and x values both begin in row 2 (I normally try to use the same rows unless there is a specific reason not to). Change the CO2 series to be rows 2:196 to match the first "temp" data series, and you should fix the issue.

As an educational exercise, you will also need to instruct your students to not use full column references when they add the second data series. Many of them will think using full column references is a nice shortcut, but it doesn't work in this case.

One problem is the use of full columns to define X and Y values. This would include the header information, which is text, and therefore the x axis would be a increment rather than true value.

If you convert you data to a table you can simply add new data to the end and the chart will automatically update.