Boris,
It's hard to tell where the reason is without seeing the model. The budget analysis does a backward calculation of the boundary flows based on the resulting head distribution as a check of the resulting conditions (not just an integration of the boundary conditions that have been set). So there might be different reasons for an inflow shown:
1) If you have an extremely high number of boundary nodes with flows near 0, the summation of values at all these nodes could accumulate small errors.
2) If the solution is not stable and the head distribution near the boundary condition is not correct, the budget analysis can give strange results. In that case, this is a hint to have a more detailed look at model stability, e.g., by placing observation points near the boundary and looking at the behaviour of head/pressure.