Question: What are some real-life exceptions to the PEMDAS rule?
I am looking for examples from "real" mathematical language --- conventions that are held in modern mathematics practice, such as those appearing in papers, books, and class notes, that are not covered (or contradicted) by PEMDAS. I am not interested in contrived examples, such as those constructed [to confuse people on Facebook](https://slate.com/technology/2013/03/facebook-math-problem-why-pemdas-doesnt-always-give-a-clear-answer.html).

The PEMDAS convention says that order of operations are evaluated as:

1. Parentheses
2. Exponents
3. Multiplication and Division, from left to right
4. Addition and Subtraction, from left to right

So far I know of one exception: sometimes the placement of text indicates "implicit" parentheses: text that is a superscript, subscript, or above/below a fraction.

* $2^{3 + 5}$

Here, $3 + 5$ is evaluated before the exponentiation
* $\frac{3+5}{2}$

Here, $3 + 5$ is evaluated before the division

Are there other exceptions?

Answer: 
The examples you give aren't exceptions. The parentheses aren't needed because there is no other way to interpret the expressions.

In applications in engineering and the physical sciences, variables have units associated with them, and the units often disambiguate the expression without the need for parentheses. For example, if $\omega$ has units of radians per second, and $t$ has units of seconds, then $\sin\omega t$ has to be interpreted as $\sin(\omega t)$, not as $(\sin\omega) t$, because the sine function requires a unitless input. Omitting the parentheses is preferable in examples like these because it simplifies the appearance of expressions and makes them easier to parse.

Similarly, if a force $F$ acts on an object of mass $m$ for a time $t$, then, starting from rest, the object is displaced by $Ft^2/2m$. This can only be interpreted as $(Ft^2)/(2m)$, because otherwise the units wouldn't come out to be units of distance. Examples like this aren't just typewriter usages. Built-up fractions that occur inline in a paragraph of text are awkward typographically: $\frac{Ft^2}{2m}$. They either have to be written very small, which makes them hard to read, or they force the spacing of the lines to be uneven, which looks ugly.

These are examples involving physics and units, but more generally, when people read mathematics, they apply their understanding of the content, which could be economics or number theory. People are not computers. Mathematical notation is a human language written for humans to read. Human languages are ambiguous, and that's a good thing. When we don't require all ambiguities to be explicitly resolved, it helps with concision and expressiveness.

Besides the meaning, another factor that resolves ambiguities and allows concise and readable notation is that we have certain conventions that we follow, such as the convention that tells us to write $2x$ rather than $x2$. If someone means $(\sin x)(y)$, then they'll write it as $y\sin x$, not $\sin xy$. There is also a convention that if we have a long chain of multiplications and divisions, such as $abcdefgh/ijklm$, we put all the multiplicative factors to the left of the slash, and then it's understood that we mean $abcdefgh/(ijklm)$. We wouldn't write this as $a/ibc/j/kdef/lgh/m$, which would be extremely difficult to read. We wouldn't interpret $abcdefgh/ijklm$ as $(abcdefgh/i)jklm$, because if that had been the intended meaning, it would have been written like $abcdefghjklm/i$.
That's a good question. In addition to PEMDAS there's grouped symbols; they occur under a radical ($\sqrt{~}$, $\sqrt[n]{~}$), in the numerator and denominator of a fraction and in exponents. These grouped symbols are treated as if they are between parenthesis. That means that the expressions $a^{\text{expression}}$, $\sqrt[n]{\text{expression}}$ and $\dfrac{\text{expression}\_1}{\text{expression}\_2}$ mean $a^{(\text{expression})}$, $\sqrt[n]{(\text{expression})}$ and $\dfrac{(\text{expression}\_1)}{(\text{expression}\_2)}$.

The horizontal fractional line and the [vinculum](https://en.wikipedia.org/wiki/Vinculum_(symbol)) of the radical act as symbols of grouping. That's why we write $\sqrt{\text{expression}}$ instead of $\sqrt{~}(\text{expression})$ and $\dfrac{\text{expression}\_1}{\text{expression}\_2}$ instead of $(\text{expression}\_1)/(\text{expression}\_2)$. The exponent, written in superscript, is also a grouped symbol, so we write $a^{\text{expression}}$ instead of $a\wedge(\text{expression})$.

Other functions use parentheses around the input to avoid ambiguity. The parentheses are sometimes omitted if the input is a monomial. That doesn't have anything to do with units. Thus $\sin 2x$ means $\sin (2x)$ but $\sin a+b$ means $\sin (a)+b$. Personally I prefer to write the parenthesis even around a monomial like $\ln (5x)$. 

What does $a/bc$ means? Is it $\dfrac{a}{bc}$ or $\dfrac{a}{b}c$ ? We could argue which convention we like but the matter of fact is that different people have different convention and different softwares have different conventions. For example $18/2\times 3$ gives [$27$](https://www.wolframalpha.com/input/?i=18%2F2*3) on wolframalpha but $a/bc$ gives [$3$](https://www.wolframalpha.com/input/?i=a%2Fbc+where+a%3D18+and+b%3D2+and+c%3D3) when $a=18$, $b=2$ and $c=3$. The same software has two conventions for the same expression! That's why I always prefer to write $\dfrac{a}{b}$, $\sqrt{a}$ and $a^b$ instead of $a/b$, $\sqrt{}a$ and $a\wedge b$. They don't cause any ambiguity. The same issue is present with $\sin ab$ which WA interprets as [$b\sin a$](https://www.wolframalpha.com/input/?i=sin2*3) or [$\sin (ab)$](https://www.wolframalpha.com/input/?i=sin+ab+where+a%3D2+and+b%3D3).