Self Assessment Taxed Twice ?

Good Morning, I am trying to do my Self-Assessment but there seems to be an issue I do not think is correct. I am employed and have an Armed Forces pension; both must be added as Income of course. My wages are taxed at X and my Armed Force pension is taxed at SD1. When I get to view my calculation after inputting it all, it says I have to pay back £1.8k, this surprised me, so tried to work out what caused it. When I removed my Armed forces pension it said I was due back £500, added it back £1.8k again. So my question is if both are taxed at source, why does it add both figures together and say I am due money to HMRC ?, but when I remove my Armed Forces pension the money turns to a positive ?. I could maybe understand my wages being an issue going up and tax code changes. Thanks for any feedback.

Hi,
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