The transaction MB5T shows negative Stock In Transit for a Cross Company Stock Transport Order (Inter Company).
In Intra-Company Stock Transport Orders there is "real" stock in transit: When the goods issue is posted from the supplying plant the system updates the stock in transit in the receiving plant (MARC-TRAME).
In Cross-Company Stock Transport Orders there is not "real" stock in transit: When the goods issue is posted from the supplying plant there is not any stock update in the receiving plant. The goods issue in the supplying plant is totally independent of the goods receipt in the receiving plant.
In this case the stock in transit is only "virtual": it is dinamically calculated by the program via the purchase order history, as the difference between the goods receipt and the goods issue quantity. Since we do not have any real stock in transit updated in any table, it can indeed be negative, when, for example, the goods receipt is posted before than the goods issue.
Related notes / content:
25220 No stock in transit with cross-company purchase orders