You may find reading interesting this article Article Theoretical and Methodological Problems of Historical Resear...
The main problem and challenge is anachronism: using our contemporary values to research the past.
In the last 50 years - at least - the concept of "objectivity" was erased from history (historiography) and social sciences. Since these are conceptualization sciences, validation is made through an intersubjective process: what you research and publish will only be valid through the readings, discussion, and criticism within the scientific field. There is no a priori or methodic "objectivity". It simply doesn't exist in the epistemology of social sciences, and nowadays history clearly is the set of social sciences researching the past.
Some researchers take for truth historical findings without analyzing them from a global or more complex point of view. Also, they isolate people, towns, or events as if they stood alone in past years and not relate them with a wider world.
http://www.soeagra.com/ijert/ijertdec2012/6.pdf This paper is a bird-eye account of the challenges of historic research... I hope it will help to you partially Ahmed Hasan Sahib Al-Battat
these are mainly general problems ,are there any specific problems of chronology in historical research/
The observation of Dr. Francisco Albert Tapia is valid. The events should be placed in their proper historical context. The writers/researchers/historians should consider and examine the historical circumstances surrounding an event. They should relate an event to a broader historical milieu.
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