From: Georgetown, Texas, USA
Yes there is an issue.
AI sub operations has a check to determine if a given sub should be used offensively or defensively. This check looks at sub size (tonnage), endurance, diving depth, and number of torpedoes. The cut off point for each increases year by year. The intent is to let marginal subs (like the US Old-S class and most Japanese RO boats) be used offensively for the first year or two of the war, then slowly be retired into defensive roles. For all the allies, most older boats (even the mid 1930s classes) were withdrawn by late war and the checks were aimed at accomplishing this.
Problem is with the details of the checks, which are a tad over-stringent. Based on a number of factors, the threshold crept up such that Gato class subs at bases far behind the lines will be tagged "defensive". Requires a number of demons to line up properly, but it will happen. It also points out how few players play against the allied AI and get their games into 1944/45. The routine needs some tuning.
Only solution for now is to break into the AI now and again, check for subs held up at major rear area bases (San Francisco and maybe Balboa and/or Columbo), and manually send them forward. For San Francisco, make sub patrol TFs with as many subs as will fit, give them a home port of Pearl Harbor, and select auto-disband.