If the IRS says that you did not file a request for extension, it's unlikely to appear in your account transcript since the IRS is looking at the same transcript. If the transcript of your account record does not show receipt of a timely filed request for extension, one way that you might be able to establish that you actually filed one would be if you had a USPS receipt documenting the mailing of Form 4868. If you used IRS DirectPay, you might be able to substantiate the request for extension with a bank statement showing the debit of the payment from the account.
If you file as married filing jointly, also check your spouse's account transcript in case the IRS failed to look at that.
