Hi Teague,
Welcome to the Bachido Forum!
Ah yes. I think most all shamisen players (including myself) have had this problem too. I assure you it’s not because of it being a nagauta style (assuming you have a correct bridge in place). Wielding the giant plectrum to strike one specific string takes time to build coordination.
At first, I would advise taking a minute (or a few minutes, as long as you don’t get frustrated) to slowly and intently try pressing down on one string. You can look directly at your bachi to make sure it’s touching the right one.
Basically, take it slowly. If you can confidently strike the desired string at a slow speed, bring the speed up a bit.
Also, I encourage posting a video of your problem. It can help myself or others diagnose your question more accurately.
Again, great to have you here!
All the best,
Kyle Abbott