This is a known behavior. You may have a clean issue checker when editing and then have issues show up when you try to deploy, or have "hidden" issues only appear later when editing and navigating around your app.

The workaround here while we look to improve this experience is to click around your app and visit pages and elements after editing them. To flag issues, Bubble does a lot of calculations behind-the-scenes. For very large apps, this calculation may spot additional issues on a page only once you visit that page.