Mistakes that cost you the refund

Under the new system you have already paid the tax. Any of these mistakes means you simply do not get it back.

Checking in your suitcase first. The check must be done before baggage drop. Checked bags cannot be taken back.
Missing one item from a receipt. The check works per receipt. If one item is missing, nothing on that receipt is refunded.
Opening or using consumables. Food, drinks or cosmetics used in Japan mean the receipt cannot be refunded. Tell customs at the counter instead of using the kiosk.
Leaving more than 90 days after purchase. The check must be done within 90 days of the date of purchase.
Arriving too late. If you stop a red-result inspection to catch your flight, the check does not count, and missed flights are not compensated.
Doing the check at the wrong airport. On a domestic-to-international connection, only the last airport in Japan counts.
Not registering a refund method. If you skip the registration the shop explains, the money has nowhere to go.
Buying more than you can carry. Tax-free purchases are limited to what you can take out of Japan yourself.
Not taking the goods abroad after the check. The tax is collected again and penalties can apply.

Simple habit that prevents most problems

Keep tax-free purchases in one bag, grouped by receipt, unopened, and do the kiosk check as the very first thing at the airport.