When I use a clipping mask in Illustrator on a PNG, there was a warning message that the colours may be not as expected in transparency along with a button to Continue. Another time there wasn't any message. My question is:

Is there any problem in using clipping masks in Illustrator in designing t shirts or anything will be printed?

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There is no problem using clipping masks in an artwork for print - whether that's print on t-shirts or anything else.

However, artwork produced for print is almost always CMYK (or CMYK + spot) and the PNG format only supports RGB.

With that in mind, there would be colour shifts if you attempted to print out a file with a PNG in it.

The warning you describe is just that, a warning, letting you know that you've got non-process (non CMYK) colours in your artwork which will shift if you attempt to print them as process colours.

(It's also worth checking the resolution of your PNG and making sure it is going to print well enough too.)

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