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Staples in passport pages used to be very common - many countries would staple a form into your passport on entry, which would then be retained when exiting the country (for example, the US used to do this with I-94/I-94W forms, but they are far from the only ones). This practice is less common today, but I'm sure there are still some countries that do it.
Consulates and immigration staff know this, and will not pay any attention to a staple hole in a passport when it comes to using that page.
If the staple holes have led to, for example, a tear in the page or something that is more visible than a few holes then it's possible the answer would be different - but for simple staple holes you will not have any issues at all.