It's their algorithm. It appears that they are using an inaccurate constant of 3.3 to back into the number of chalakim from the number of seconds. This constant should instead be 3 + (1/3). Most of the time this is okay, but if the intermediate result aligns just right, an error is introduced that produces the wrong number for the chalakim result.
Artscroll have one here: https://artscroll.files.wordpress.com/2021/12/mishnah-yomi-calendar_download.pdf
They also have one just for Zeroim here: https://artscroll.files.wordpress.com/2021/12/mishnah-yomi-calendar_zeraim_download.pdf