There is a TurboTax FAQ for FSA's: <a rel="nofollow" target="_blank" href="https://ttlc.intuit.com/questions/1901348-what-is-a-flexible-spending-arrangement-fsa">https://ttlc....>

IRS Publication 969 (<a rel="nofollow" target="_blank" href="https://www.irs.gov/pub/irs-pdf/p969.pdf">https://www.irs.gov/pub/irs-pdf/p969.pdf</a>) states:
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Note. Unlike HSAs or Archer MSAs which must be reported on Form 1040 or Form 1040NR, there are no reporting requirements for FSAs on your income tax return.
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There is a limit to how much an employee can be put aside tax-free into an FSA.  For 2017 it was $2600.  For 2018 it increases to $2650.  Your employer handles this aspect.  An employer can optionally choose to contribute more than that limit.

In the event that an employee chooses an FSA withholding rate that causes the limit to be exceeded and the employer makes a reasonable mistake in failing to catch it, the excess would then appear as W-2 income to the employee.  (<a rel="nofollow" target="_blank" href="https://www.irs.gov/irb/2012-26_IRB#NOT-2012-40">https://www.irs.gov/irb/2012-26_IRB#NOT-2012-40</a>)

There is a specific reason I'm concerned.  We file our returns as married-jointly.  My wife has an HSA through her work and I've heard that she is not supposed to be eligible for that if I have an FSA through my work.  My son is insured through my wife's insurance, and I am the sole person on my insurance.  Turbotax has not flagged this issue, so I'm totally confused as to whether or not we have an issue or not

<a rel="nofollow" target="_blank" href="https://www.irs.gov/publications/p969">https://www.irs.gov/publications/p969</a> is where you can look for the eligibility criteria and what to do about excess contributions.  (Still waiting for them to post their 2018 PDF version.)

I have entered all of my Childcare expenses for three children that qualify 

my qualifying Childcare expenses are $20,000

initially Turbo tax is telling me that we get a $1,200 tax credit - but I know this is not correct because I will loose $1,000 of this credit because I contributed and used $5,000 to a flexible spending account for dependent care via my employer

Where in turbo tax do I enter FSA dependent care dollars so it will properly reduce my child care tax credit down to $200 by reducing the $6,000 of expenses to be consider by the $5,000 FSA deductions from my paycheck ( can not double dip ) so that only $1,000 is considered for the tax credit which in my case will be a $200 tax credit

If my employer has not deducted my FSA from my gross wages, where do I enter that on my 1040 tax form?

These contributions are generally reported in box 12 of your W2 and reduce box 1 wages.  If this was not reported correctly by your employer, you will need to request a corrected W2.  There is no way to deduct these amounts on your return.