Can having a pending Express Entry profile be used against me at the border as proof I won't leave?

Not on its own. Having a pending Express Entry profile is simply a normal expression of interest in eventually immigrating to Canada through one of the federal economic programs it manages, and dual intent means this cannot automatically be treated as proof that you will not leave Canada at the end of an authorized temporary stay. A border officer is not permitted to refuse entry, or a period of authorized stay, purely because of a pending profile.

That said, a border officer would still need to be satisfied on the whole picture that you meet the requirements for the specific temporary entry being sought, and a pending Express Entry profile is simply one fact among many that could be considered alongside other, independent reasons for concern, if any genuinely exist. It is not, by itself, a red flag under dual intent, but it also does not exempt an applicant from the officer's broader assessment.

Anyone concerned about how a pending Express Entry profile might come across at the border should be prepared to explain their travel plans clearly and honestly, without feeling the need to hide or minimize the profile's existence.