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"methodological challenges" is a correct and usable phrase in written English.
It is typically used to refer to the challenges associated with research methodology and design. For example, "This study highlights challenges posed by multiperspectivity, such as methodological challenges in measurement and interpretation."
Exact(60)
There will be some serious methodological challenges to doing that, of course.
Methodological challenges also abound.
This added complexity poses significant methodological challenges.
The comprehensive approach evoked methodological challenges.
Such approach faces three main methodological challenges.
Methodological challenges of this study are discussed.
This presents methodological challenges for the field.
Identification of areas at risk presents methodological challenges.
The paper will outline some of the methodological challenges.
However, VCO2-based calorimetry has two methodological challenges.
These approaches, however, face a number of methodological challenges.
More suggestions(15)
methodological threats
procedural challenges
conceptual challenges
methodological constraints
systemic challenges
methodological problem
methodological change
way challenges
approach challenges
ways challenges
technique challenges
methodological difficulty
process challenges
methods challenges
methodological task
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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