Please make sure that when you are ready to save the project in pdf format you include an 1/8 inch bleed on all sides, even if one side doesn't bleed. It is necessary in order to keep the artwork centered to include the same bleed on all sides.
Please make sure that when you are ready to save the project in pdf format to select the CMYK color mode. Convert all spot colors to CMYK if the job doesn't require them. In Photoshop select Image > Mode > CMYK.
Please make sure that when you are ready to save the project in pdf format you flatten all transparent objects. In photoshop Merge all the layers under the Image tag. In Illustrator make sure to unlock all items and then select all of your artwork by clicking the Select tab and choosing the Select All option, then click the Object tab and choose Flatten Transparency, Select the preset [High Resolution] and press OK.