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The phrase 'there were shortcomings' is correct and usable in written English.
It is often used to indicate that something did not meet expectations or failed in some way. For example, "There were some shortcomings in the way the project was managed, but we still managed to achieve our goal."
Exact(29)
Others were disappointed and felt there were shortcomings in treatment, service and accessibility.
But he said there were shortcomings.
In any case, they heard speakers complain that there were shortcomings in existing hate-crime laws.
But the official added that there were shortcomings on the Pakistani side as well.
There were shortcomings, however, and superficially Swann was one of them.
He told Iranian reporters that he mobilized his own coalition because "we felt there were shortcomings in both other groups".
Similar(31)
But there are shortcomings.
"There are shortcomings, but not fundamental shortcomings," he said.
And there are shortcomings even in higher education.
There are shortcomings both of local education and local content.
If there are shortcomings our front-line staff are the first to see or hear them.
More suggestions(16)
there were flaws
there were difficulties
there were drawbacks
there were glitches
there were insufficiencies
there were shortages
there were weaknesses
there were defects
there were shortfalls
there were shortcomings
there were loopholes
there were gaps
there were things
there were problems
there were sins
there were leaks
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com