Which version of the game do you have? If a disk version, is it by chance the earlier v1.3x of the disk, or the v1.5 "Silent Hunter: Wolves of the Pacific - Gold Edition"? The older versions of the game did have config issues with repeating mission assignments. That was "fixed" in v1.4 and v1.5 - however, there are quite a few of those missions, and the game can seemingly still get stuck in that routine, especially inserting agents and/or spys and/or troops on Honshu, of which I have not found any historical basis on that, but they can be fun to do. There is only one assignment on the east coast of Japan that is slightly difficult, in that they put you within range of a set of shore guns, but if you are aware of that particular mission, you can approach shore from the north, using the land mass as a view block to surface and land your charge. Slink away afterwards, no matter the mission, and either then go sink some ships, or fone home with a Status Update and get another assignment. I do not like the Insertion missions, nor the PhotoOp ones that have you go into the Inland Sea. Some of us refer to those as "Hollywood Movie" assignments. Definitely not based upon fact. No matter which version of the game you have though, you can ignore orders and just go sink ships. Just be sure you sink enough to earn enough renown points. Also, you do have the likelihood of being reassigned that same mission if you did not complete that original Objective because, after all, orders are orders... snap to attention when you say that!
lol
If you have a v1.3x version of the disk game, you can use the
Official v1.4 patch from here on the SubSim site (Ubisoft no longer has that available), to update your v1.3 to v1.4, which improves the game in many ways. There are not many mods anywhere that are v1.3 compatible, and not many more that are v1.4 compatible, though there are more of those. SH4 with the U-Boat Missions, aka: Gold Edition or v1.5 is the most common version, with most of the mods available these days being written for it. If you have the Steam version of the game, there is the "Silent Hunter: Wolves of the Pacific" version, which in reality is v1.3, and then there is the "U-Boat Missions Add-On", which you need that first version for... The Steam version will not update with the Ubisoft v1.4 patch, only with its own version of the "U-Boat Missions Add-On". Ubisoft only sells a downloadable "Gold Edition" anymore.