Model-based product line engineering applies the reuse practices from product line engineering with graphical modeling for the specification of software intensive systems. Variability is usually described in separate variability models, while the implementation of the variable systems is specified in system models that use modeling languages such as SysML. Most of the SysML modeling tools with variability support, implement the annotation-based modeling approach. Annotated product line models tend to be error-prone since the modeler implicitly describes every possible variant in a single system model. To identifying variability-related inconsistencies, in this paper, we firstly define restrictions on the use of SysML for annotative modeling in order to avoid situations where resulting instances of the annotated model may contain ambiguous model constructs. Secondly, inter-feature constraints are extracted from the annotated model, based on relations between elements that are annotated with features. By analyzing the constraints, we can identify if the combined variability- and system model can result in incorrect or ambiguous instances. The evaluation of our prototype implementation shows the potential of our approach by identifying inconsistencies in the product line model of our industrial partner which went undetected through several iterations of the model.