It could be that Engine only tracks one target at a time, as a default. I don't know about VUforia Engine SDK integration with Flutter, but you can set the number of simultaneous tracked images with the Engine API.

vuEngineSetMaximumSimultaneousTrackedImages(VuEngine* engine, int32_t maxNumberOfTargets);

Just note that only image-based targets support simultaneous tracking. Model Targets and Area Targets can only be tracked one at a time. This article has more information: Detect and track targets simultaenously.