Hi Ruby,
I was very confused by the instructions with the travel form, the message I received stated that both my partner and I needed to fill out separate ones, and there were two spots open in my application. However as you noticed the form itself clearly states it should only be filled out by the principal applicant, and there is a space for the spouse's travels, so the request for 2 separate forms makes no sense!
I ended up calling CIC on the phone and they agreed that the instructions in the message did not align with the instructions on the form, and that I should just fill out one form (with my travels, and my spouse's travels in the appropriate section). Then, they suggested I write a letter of explanation explaining that I filled out the form in accordance with the instructions on the form and to contact me if they needed any more details, and upload that in the second spot. They said it made no sense for my spouse to fill out a form that clearly states it can only be filled out by the principal applicant and that my confusion was understandable.
If you're looking for confirmation on this, I'd recommend calling up CIC- they were very helpful on the phone once I managed to get through to them.
Best of luck!