If I am expected to get a refund and due to a rejection I filed an extension which was approved then everything gets sorted and I file my taxes is there a penalty ?

[niclyn4kids]

After I filed they were accepted and I received my refund but not all of it. I don’t get it

[mesquitebean]

There is no penalty on a late Federal return if one is due a Federal refund.

Did you use the Free Edition?   If so, there should be no fees to account for your difference, unless you upgraded to PLUS then chose to pay the fee out of your Federal refund.

Also, if you had a state refund, it comes separately, so be sure you are not adding the Federal and state refunds together.    Your Federal refund amount is shown on your Form 1040, Line 35a.

 Is there any message when you use the IRS "Where's My Refund" tool?

https://www.irs.gov/wheres-my-refund

If the IRS reduced your refund, you should be getting a letter from them in about 3 weeks or so, explaining why and your options if you disagree.

Here are some reasons why your refund might be less than what was shown in TurboTax.   See this FAQ:

https://ttlc.intuit.com/turbotax-support/en-us/help-article/tax-refund/refund-direct-deposit-check-l...