Which layout features most often cause ATS reading problems?

The features that cause the most trouble are those that separate text from the normal top-to-bottom flow of the page. In rough order of risk:

• Text boxes and shapes holding important text, such as your name, contact details or a whole section.
• Sidebars and multi-column layouts, which can be read out of order or line by line across columns.
• Tables used to position content, where cells may be read across rows rather than down columns.
• Text placed in images, banners, icons or charts, which software cannot reliably read.
• Content in Word's page header or footer, which some systems handle poorly.
• Design-app PDFs that store each word or line as a separate positioned piece.

None of these automatically ruins a resume, and some systems cope with them well. But each one adds a chance that your information is misread, and you cannot know in advance which system an employer uses.

The practical answer is to keep your core content (name, contact details, work history, education and skills) in a single column of normal text, and to check your final file with the copy-and-paste test: select all the text in your PDF, paste it into a plain text editor, and confirm everything appears in a sensible order.