Apart from simplified characters that merge two traditional characters into one, as already pointed out (and there are quite a few of these -- 後 and 后 merged into 后 is one example, 裏, 里 and 裡 merged into 里 is another, 鵰 and 雕 merged as 雕 is another), I couldn't offhand think of any cases where a simplified character has the same form as a completely different traditional character, but ahkow found two (see answer below):
葉 > 叶 (Mandarin yè; leaf)
聼 > 听 (tīng; to listen)
where 叶 was xiè（to make something sound good/euphonous) and 听 was yīn (as an adjective to describe someone smiling) before simplification.
Theoretically merged characters could lead to ambiguity. For example:
他射了學校裡的大鵰. Traditional: He shot a large eagle in the school.
他射了学校里的大雕. Simplified: Either 'He shot a large eagle in the school' or 'He shot a large statue in the school'.
他射了學校里的大雕. Mixed. By throwing 學 in there, you are opening the door to potential confusion. To a person familiar only with traditional characters, this could be interpreted as 'He shot a large statue in school village' (里=village). To a person familiar with simplified characters (but knowing the character 學 as the traditional form of 学), it would be: 'He shot a large statue in the school' or 'He shot a large eagle in the school'.
So theoretically the choice of one character set or the other does imply certain choices and interpretations, and mixing the two can lead to confusion.
That said, users of traditional characters do use simplified forms in handwriting -- because that's often what the simplified characters were originally based on! So in handwriting, it would be perfectly ok for a person from Hong Kong or Taiwan to write, say, 他進了校门, because 门 is a simplified form of 門 that has long been current in ordinary Chinese handwriting. There are also people on the Mainland who sometimes mix traditional characters into their writing because they happen to prefer the traditional form.
The creation of an officially defined 'simplified character set' has in some ways interfered with the older fluidity that existed in writing. What it has done is set in stone the choices to be made (either Traditional or Simplified, and no mixing of the two), making it harder to simply use the form of character suited to the circumstances -- full forms in careful or official writing, simplified forms in casual handwriting.