Supporting the execution of transactions through the use of electronic documents requires security. The scope of this security primarily involves ensuring the integrity, authenticity and non-repudiation of the origin of information. The signed XML document is a powerful tool that ensures the above features and the ease of processing and integration with various systems. An XML document may have many signatures, and each of them may sign different parts of the document. This feature is highly attractive, but in order to use it, the signature and structure of the document must be carefully designed. This article presents the existing risks associated with the use of XML signatures, focusing on XML signature wrapping vulnerability. This vulnerability is a consequence of the relationship between the XML signature and the signed document. The authors suggest that without neglecting the need for protection against the possibility of moving and replacing a fragment of the document, the use of secure XML signature references should also be considered and applied. The article proposes the use of secure signature templates as a countermeasure against the threat of an improper indication of the signed content defined in the signature reference. This threat is serious in automatic signature processing, where it is important to correctly indicate the signed content.