The BBC article focuses on elections in Africa, but the red flags are probably close to universal.
Too many voters
Watch the turnout figures ‒ they can be a big giveaway.
You never get a 98% or 99% turnout in an honest election. You just don’t.
Voting is compulsory in Gabon, but it is not enforced; even in Australia where it is enforced, where you can vote by post or online and can be fined for not voting, turnout only reaches 90-95%.
The main reason that a full turnout is practically impossible is that electoral registers, even if they are recently compiled, can rarely be 100% up-to-date.BBC News
A high turnout in specific areas
Even where the turnout is within the bounds of possibility, if the figure is wildly different from the turnout elsewhere, it serves as a warning.
Why would one particular area, or one individual polling station, have a 90% turnout, while most other areas register less than 70%?
Something strange is almost certainly going on, especially if the high turnout is an area which favours one particular candidate or party over another.BBC News (original source)
Large numbers of invalid votes
There are other, more subtle ways that riggers can increase votes ‒ or reduce them.
Keep an eye on the number of votes excluded as invalid. Even in countries with low literacy rates this isn’t normally above 5%.
High numbers of invalid votes can mean that officials are disqualifying ballots for the slightest imperfection, even when the voter’s intention is perfectly clear, in an attempt to depress votes for their opponents.
More votes than ballot papers issued
When the polls close, and before they open the boxes, election officials normally have to go through a complicated and rather tedious process known as the reconciliation of ballots.
After they have counted how many ballot papers they received in the morning, they then need to count how many are left, and how many ‒ if any ‒ were torn or otherwise spoiled and had to be put aside.
The result will tell them how many papers should be in the box. It should also match the number of names checked off on the register. The first task when the box is opened is to count the number of papers inside, this is done prior to counting the votes for the different candidates.
If there is a discrepancy, something is wrong. And if there are more papers in the boxes than were issued by the polling staff, it is highly likely that someone has been doing some “stuffing”.
That’s a good enough reason to cancel the result and arrange a re-run.
Results that don’t match
Mobile phones have made elections much more transparent.
It is now standard practice to allow party agents, observers and sometimes even voters to watch the counting process and take photographs of the results sheet with their phones.
They then have proof of the genuine results from their area ‒ just in case the ones announced later by the electoral commission don’t match.
It has clearly taken crooked politicians some time to catch up with the fact that people will now know if they change the results.
Delay in announcing results
Finally something that is not necessarily a sign of rigging, but it is often assumed to be so.
Delay is certainly dangerous, fuelling rumours of results being “massaged” before release and increasing tensions, but this is not incontrovertible proof of rigging.