The organization has not been recognized with the tax-exempt status by the IRS. Only exempt organizations can file Form 990.
The organization must have an exempt status to qualify for filing a 990 return. In this case, the IRS would have rejected the return under these scenarios.
If the organization has filed its Form 1023 application with IRS, they need to wait until the IRS grants exempt status to the organization before filing Form 990. If the IRS has rejected the return despite the organization having the exempt status, then we suggest you contact the e-help Desk Toll-Free Number 1-866-255-0654.