Either route a notch, like I show in the bottom corner, or drill a hole, like I show in the top corner, for clearance.
You can upgrade to V Carve Pro, which handles this automatically. From their website:
Bone Filleting corner filleting options are available that help ensure parts cut from sheet materials will slot together after cutting.
The 'Dog-Bone' and 'T-Bone' fillets allow toolpaths to ‘notch’ the inside corners of slots and grooves, allowing mating parts to fit flush against the true base of the pocket. This technique allows the radius of the cutter to be removed from the bottom of slots.
These filleting tools are perfect for designing and machining furniture, cabinets and model aircraft components etc. where precision fit is needed.