One-dimensional Majorana modes are predicated to form in Josephson junctions based on three-dimensional topological insulators (TIs). While observations of supercurrents in Josephson junctions made on bulk-insulating TI samples are recently reported, the Fraunhofer patters observed in such TI-based Josephson junctions, which sometimes present anomalous features, are still not well understood. Here we report our study of highly gate-tunable TI-based Josephson junctions made of one of the most bulk-insulating TI materials, BiSbTeSe2, and Al. The Fermi level can be tuned by gating across the Dirac point, and the high transparency of the Al/BiSbTeSe2 interface is evinced by a high characteristic voltage and multiple Andreev reflections with peak indices reaching 12. Anomalous Fraunhofer patterns with missing lobes were observed in the entire range of gate voltage. We found that, by employing an advanced fitting procedure to use the maximum entropy method in a Monte Carlo algorithm, the anomalous Fraunhofer patterns are explained as a result of inhomogeneous supercurrent distributions on the TI surface in the junction. Besides establishing a highly promising fabrication technology, this work clarifies one of the important open issues regarding TI-based Josephson junctions.