ALMA has long had a policy that the fonts used in the Scientific Justification PDF should not be smaller than 12 points. This is to ensure fairness during proposal review i.e. so that all proposals have the same amount of text available to make a scientific case. The Observing Tool will examine the PDF and establish what fraction of the text has a size less than 12 points. From Cycle 8 2021, a threshold has been imposed such that >15% of the text must be smaller than 12 points before an error is displayed, which prevents the proposal from being submitted.
In checking the font-size fraction, the OT will consider every occurrence of a text character in the PDF. This will include figure axes and annotations, table captions, etc. The OT will also see "hidden text" that may not be displayed because, for example, it was cropped out of a larger figure. This can happen, for example, using Preview on a Mac using the rectangular selection tool and CMD-C (copy) and CMD-N (create new). This preserves the vector graphics, but retains all the text on the page in hidden form. If the OT is complaining about the font sizes being too large and the reason is not immediately clear, it might be related to these issues.
Simply taking a screenshot of the desired figure (CMD-Shift-4 on a Mac) will avoid this issue. Another solution is to convert the PDF to another format e.g. jpeg.