XML was originally meant to be a document markup format, an evolution of SGML. While the markup was consistent, the interpretation of it was to be left to the actual document format definition.
Unfortunately, there was another camp which was trying to change it to not just be an extensible document interchange format but a data interchange format. These have different requirements.
For example, someone asked when you put data in an element vs an attribute. There was a push to provide guidance at one point based on SVG - everything other than text data (such as coordinates making up graphics) were attributes, such that a non-SVG view of the document would just be all of the textual data appended.
Most of the tooling issues came from this disconnect between document and data oriented interchange, such as tooling having options to toggle between interpretations of pretty fundamental concepts such as namespaces.
It also became pretty common for technologies to come out of the document-oriented space (e.g. XPath and XSLT) which led to it being basically impossible to compose or decompose XML-based data without potentially changing its meaning - unless you were doing so with tools that understood the interpretation of the data itself.
Unfortunately, there was another camp which was trying to change it to not just be an extensible document interchange format but a data interchange format. These have different requirements.
For example, someone asked when you put data in an element vs an attribute. There was a push to provide guidance at one point based on SVG - everything other than text data (such as coordinates making up graphics) were attributes, such that a non-SVG view of the document would just be all of the textual data appended.
Most of the tooling issues came from this disconnect between document and data oriented interchange, such as tooling having options to toggle between interpretations of pretty fundamental concepts such as namespaces.
It also became pretty common for technologies to come out of the document-oriented space (e.g. XPath and XSLT) which led to it being basically impossible to compose or decompose XML-based data without potentially changing its meaning - unless you were doing so with tools that understood the interpretation of the data itself.