That's a question that is specific to your use case and why you have the problem that you do.
First, there is the question of if your users have a reason to use zoom as a rule. I know it's not one of the normal "checklist" things to account for, so unless your users have a specific reason that this is likely, it's probably a low priority to address.
Second, other than not looking "right", does it cause a functional problem on the page. Certainly, if you were starting the project, I'd say you should address it if it isn't time-prohibitive. However, at this stage, there's the question of how big of a priority it should be and unless it has a real impact on using the site, that might be low.
Lastly, though very importantly, why is it doing that? Is it an odd artifact with zoom or is it a problem with how your page's DOM is organized. If some components of your application are constrained differently than others, you might have a problem that becomes much more impactful as resolution and device norms change over the next few years. This would significantly raise the importance of addressing it sooner rather than later.