I was charged a penalty from the IRS for failure to file my partnership return on time. But Turbotax says my 2024 return was accepted. What did I do wrong?

"Accepted" does not mean it was filed on time.  Accepted means you entered enough information for the IRS to take it into the system for processing.

https://turbotax.intuit.com/tax-tips/small-business-taxes/business-tax-deadline-guide-for-2024/c6DlyOhp5

Partnership returns (and S Corps)  were due on 3/17/25. This differs from individuals or sole proprietor taxpayers. 
Look under the File menu, Electronic Filing, Show Electronic Filing History to check the file date. 

if you filed after 3/15/2025 with no extension, you may want to request the IRS to abate the penalties if this is the first time you've filed a 1065 or all others were timely filed. The decision is in the hands of the IRS.