One of the hardest things to understand about military pay is that while it is paid twice a month (usually), it is calculated on a monthly basis.
Back in the dinosaur ages, military pay was paid one time per month. At the end of the month, the finance folks would calculate everything due for the month and pay it at one time. With the addition of twice-a-month pay, they had to figure out a way to calculate the amounts. For the mid-month pay, the finance folks estimate what the end-of-month figures will be, then pay half in the mid-month pay.
At the end of the month, your friends in finance tally up all your pays and allowances, just as if you were being paid once a month. They then subtract the amount that was paid in the mid-month pay to figure out how much you will receive in your end-of-month pay.
In theory, this should work well and you should receive two roughly even paychecks each month. In reality, lots of things can happen between the mid-month calculations and the end-of-month calculations. You can be promoted, your pay can change due to time-in-service, you can be deployed to a combat zone, you can become eligible for Family Separation Allowance (FSH), you can become eligible or ineligible for BAH, etc. As a result, sometimes the actual end-of-month figures aren't even close to the estimates used to calculate your mid-month pay. When this happens, you'll find your end-of-month pay is different from your mid-month pay.
This is the reason that you only receive a Leave and Earnings Statement (LES) with your end-of-month pay, and why your LES shows your mid-month pay as a deduction.
Understanding how the system works is the first step in making sense of military pay. Once you have some experience understanding your pay and LES, you'll be able to predict how certain events will affect your pay. You'll also be able to see if there have been mistakes made, and explain the mistakes so that they can be corrected.
May LES should be released today. Have a look, and see if this all makes sense.