TurboTax is saying I over contributed my HSA and wants me to withdraw the money. This is incorrect because I changed to Family plan which allows for higher contributions.

[car1234]

I contributed to my own HSA to the limit as Self plan. My wife changed from Self Plan to Family Plan mid-year and her contribution to her own HSA was above the Self Plan limit, but lower than the Family Plan limit.

[Opus 17]

That sounds very confusing.  Remember that the family plan limit is shared -- you can divide it between the two of you but your combined total can't be more than either of your individual totals.  in other words, if you were covered by a family plan for the whole year, your combined maximum is $8550 total, not $8550 each.   Or, if you each had single covered from January to June and switched to family coverage in July through December, your individual limits would be $6425 (or $8550 if you use the last month rule) but your combined contribution can never be more than $8550.

For which months were you covered by a single, or family HDHP?  (Covered means you are covered by the plan, even if you are not the subscriber.).   How much did you contribute?

For which months was your spouse covered by a single, or family HDHP?  How much did she contribute?

Are either of you over age 55?

[car1234]

Just to clarify, I'm not in the same plan as my wife, we both have separate insurance and separate HSA accounts.

Shouldn't the limits be calculated separately in this case?

For me, I was covered on single HDHP all year. I contributed $4300.

For my wife, she was covered on single HDHP half the year and the other half on family HDHP. She switched her plan after we had a baby, but I'm still not in her plan. She contributed $8550.

No one is over 55.

[Opus 17]

Your personal limit is $4300, your wife's personal limit is $8550 if she relies on the last month rule, or $6425 if not using the last month rule.  But your combined limit will never be higher than $8550.  The limits don't stack.   

See publication 969, page 7, rules for married people.