Only with our very beloved ones, we might be rude for a isolated remark, as in this case, because there is much love and respect which put things by another perspective.
Usually, when familiar relationship are too bad, you'll see ice floating in the air, and this hasn't ever been the case for The Queen and Queen Sofia.
If she had spoke that way to a member of the public or to a courtier, I had considered the gesture rude and vulgar, but QS is her mother in law, very much respect and loved for many many years.
I would blame first the protocol of the event, I did never seen a Royal Family having to descend the nave of a church, among thousands people standing up upon the pews, screaming and recording any details with their phones. The atmosphere was panicking and, moreover, Queen Sofia is quite deaf, and the Queen had to spoke loudly. The Queen lose control of herself for a second, because it is clear that her intention was only that of inviting granny and kids to have their photo outside, with a better surrounding.
The media development has the issue taken, I'm sure is very painful for all the royals involved, for both queens and sadly also for The Princess, who has no blame at all, but when one is young is more sensitive and easy at tacking the blame, especially if something hurt your grown ups.
I really hope that all this will be forget quickly. In Spain we have many more serious issues, than an annedoctic and unimportant "quarrel" in the Royal Family.
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