I think the main problem is the knowledge of pilots regarding which countries have and which countries haven't filed a difference to the ICAO Standard.
As we know, according to 'The Standard', most countries in the world require ATC to specifically cancel any altitude/FL restrictions if they instruct you to climb/descend in a manner differing from the SID or STAR. If they don't say anything then you must comply with those restrictions.
However, not everyone is in the same boat and, as an example, the UK, USA and Japan do things differently. The USA can now tell you to climb or descend, in which case you do so without restriction, but if it's a 'climb via the SID' then you must comply. The UK & Japan are more simple in that unless you're specifically told to comply with the restrictions then ATC's instructions overrule the SID/STAR and you can ignore the hold downs/ups.
It's daft that countries file differences and there really should be one standard. It is also daft that pilots fly into other countries without knowing what the local rules are. However, trying to find those differences is often more difficult than it should be and I've found Jeppesen do not do a particularly good job of highlighting differences such as this.