When a compound is still in the column at the end of the run due to higher retention, it will elute in the next run. You will know if you do a blank injection, and you will see a peak that shouldn't be there because there is no analyte in the blank. To make sure all your peaks are eluted during your run time, increase the run time and then optimize the gradient. It is always a good practice to include a blank injection in a sequence to make sure you don't have a carryover, or the S/N is adequate (the column is not deteriorating).