Those colours are called CMYK (cyan, magenta, yellow and black), the base colours for all colours used in printing. Basically, any colour can be obtained by using these in correct proportions. The marker is also used to identify the density of colours and dot formation.
You may not know the exact number of newspapers that are printed daily, but it is common knowledge that they are done so in abundance. Physically checking all the pages of the paper is not possible. For a printer, who has been doing this for years, knows what an apt CMYK looks like. If there is anything off, he/she will be able to spot it. So basically they serve as ‘printer’s marker’.