Your temperature may not be accurate if you did not take it as soon as you woke up but it should not mess up your charting for this cycle. Make sure to mark that day's temperature as a "questionable temp" in the Data section. By doing this, your questionable temperature will be displayed as a grey dot and will not be connected to your other temperatures on the chart.
(P.S. Want a highly accurate basal thermometer that's fast, fits comfortably in your mouth, and doesn't beep? Try Wink, a bluetooth basal thermometer that automatically syncs your temperatures and the time your temperature was taken to the Kindara app.)