It likely means processing is taking longer than expected as it moves through the stages. They may be looking at something a little more closely because of a specific issue with the return, although some returns are pulled at random for more processing. It "could" mean there could be a delay in your refund, but it's hard to predict. Only the IRS knows for sure what all they doing with your return.
This IRS FAQ gives some situations where it might take longer than 21 days:
https://www.irs.gov/refunds/tax-season-refund-frequently-asked-questions
If the IRS tool says it is still being processed, and if it's been longer than 21 days since an efiled return was accepted, here's how to reach a live IRS agent to inquire about the delay, although they are extremely busy due to staff shortages and all the stimulus questions on top of tax-filing questions:
IRS: 800-829-1040 (7AM-7 PM local time) Monday-Friday
When calling the IRS do not choose the first choice re: "Refund", or it will send you to an automated phone line.
- First choose your language. Then listen to each menu before making the selection.
- Then press 2 for "personal income tax".
- Then press 1 for "form, tax history, or payment".
- Then press 3 "for all other questions."
- Then press 2 "for all other questions."
- It may then ask for your SSN, but do not enter it. Just wait. If it asks for SSN a second time, still do not enter it.
- Then it will get "tired", and you'll get another menu. Choose 2 for "personal".
- Then in the next menu choose 4 for "all other inquiries", and it should transfer you to an agent but expect a long wait.
- I usually use a speakerphone so I can work on something else while waiting.
