Some UI events are handled by more than one tool. When many tools are enabled, an event may be unexpectedly handled by another tool that isn't immediately in context. For example, a map click made with the Markup polygon tool is also handled by the Identify tool: each click to add a point to the polygon also shows features at the clicked map location. One workaround is to turn off the Identify tool when using the Markup tool.
There may be other such conflicts between tools.
Look into ways of mitigating these conflicts. This was mitigated for the Geoark tool in pull request #156.