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Two things:

1. The global plan is only a suggestion. It may help a local planner make some decisions, but (in general) the local planner is not required to use it at all.

2. By setting combination_method=99, you are telling the global_planner to ignore anything in obstacle_layer. Why does it surprise you that in the resulting global plan, the robot footprint might the pass over an obstacle? Note this won't be an actual problem if the local_planner is able to deviate from global plan to avoid the obstacle.

Two things:

1. The global plan is only a suggestion. It may help a local planner make some decisions, but (in general) the local planner is not required to use it at all.

2. By setting combination_method=99, you are telling the global_planner costmap (and thus the global_planner) to ignore anything in obstacle_layer. Why does it surprise you that in the resulting global plan, the robot footprint might the pass over an obstacle? Note this won't be an actual problem if the local_planner is able to deviate from global plan to avoid the obstacle.