The headline makes it sound like they have engineering challenges that can't be overcome when actually the classification in this report tells us nothing new.

Here is a link to the report that they are referencing:

https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1171218/IPA-Annual-report-2022-2023.pdf

It summarizes about 150 projects in about 30 pages, so there is no specific rationale or analysis given for why each project receives the rating that they give it.

The description of the colour ratings says:

Annex A: Explanation of DCA colour ratings

The DCA is an evaluation from the IPA or the SRO of a project’s likelihood of achieving its aims and objectives, and doing so on time and on budget

...

Red: Successful delivery of the project appears to be unachievable. There are major issues with project definition, schedule, budget, quality and/or benefits delivery, which at this stage do not appear to be manageable or resolvable. The project may need re-scoping and/or its overall viability reassessed.

The HS2 projects are already over-budget (as stated in the article), so it is clear that the likelihood of achieving them on budget is zero, which makes a Red rating inevitable, and not particularly newsworthy.