This is MS.NET bug note. I confirmed them with version 1.1.

In this document I refer to OASIS test suite (by test case name).
It is located here:
http://www.oasis-open.org/committees/documents.php?wg_abbrev=xslt

No. 0001

	position() handling in predicates is incomplete. For example,
	see foo [position() mod 1 > 0] [position() > 3] [2] result 
	(match_match19, match_match22 and match_match26)

No. 0002
	Import precedence resolution on attribute sets are buggy if there are
	two imported stylesheets and both of them have identically-named
	attribute in the identically-named attribute sets. MS takes the one
	from the first stylesheet, but it must be the one from another.
	(attribset_attribset_45)

No. 0003
	http://www.w3.org/1999/11/REC-xslt-19991116-errata/ E26 says that
	attribute sets are combined before use-attribute-set is replaced with
	the actual attributes. MS does not conform to this requirement.
	(attribset_attribset42)

No. 0004
	String variable are not properly compared with strings (at least in
	some cases).
	(select_select67, select_select68, variable_variable24)

No. 0005
	MS.NET misses some kind of whitespaces.
	(Text_78273 - Text_78276, Text_78281)

No. 0006
	disable-output-escaping is not working when XmlWriter is specified as
	output. It affects on almost all output operations such as xsl:text,
	xsl:value-of, and so on.
	(Text_78308, Text_78311, Text_modified78308, Text_modified78309,
	Text_modified78311, output_output03, output_output06, output_output08,
	output_output46, output_output61, output_output62, output_output74,
	output_output75, Output_84432, Output_84433)

No. 0007
	cdata-section-elements is not working when XmlWriter is specified as
	output, like disable-output-escaping.
	(output_output28 - output_output30, output_output41 - output_output43,
	output_output87, output_output88, output_output91 - output_output98,
	output_output101 - output_output107, Text_DoeWithCdataInText).

No. 0008
	template "match" attribute does not allow variable reference.
	(match_match14)

No. 0009
	variable references are rejected inside id() function, being said that
	"It either has a variable reference or key function."
	(idkey_idkey43)

No. 0010
	id() does not consider the possibility that the argument might be a
	list string of IDs.
	(idkey_idkey57)

No. 0011
	key() does not handle variable references.
	(idkey_idkey18, idkey_idkey50)

No. 0012
	If "name" attribute of xsl:attribute is evaluated as to contain ':'
	(i.e. CName with non-empty prefix) and no matching xmlns declaration,
	MS.NET raises an error.
	(attribset_attribset15)

No. 0013
	When XslTransform output is XmlWriter (not Stream), document()
	function is not working properly.
	(copy_copy27, namespace_namespace20, reluri_reluri09 -
	reluri_reluri11, XSLTFunctions_Bug76054, XSLTFunctions_Bug76984,
	XSLTFunctions_DocumentFuncWithEmptyArg, XSLTFunctions_DocumentInUnion,
	XSLTFunctions_DocumentInUnionWithDuplicateNodes,
	XSLTFunctions_DocumentFunctionNoArg)

No. 0014
	Standard XSLT function unparsed-entity-uri() is not found.
	(expression_expression02)

No. 0015
	XPath function boolean() treats empty result tree fragment as true.
	(XSLTFunctions_BooleanFunction)

No. 0016
	If argument QName of element-available() function is expanded to
	have null namespace, it must return false. However MS.NET treats
	such one as XSLT instruction.
	(XSLTFunctions_ElementAvailFunctionTrue)

No. 0017
	format-number() does not accept some patterns.
	(XSLTFunctions_specialCharInPattern)


Not sure the reason why:
	idkey_idkey49
	impincl_impincl08
	From mdocs_mdocs01 to mdocs_mdocs18
	whitespace_whitespace35


Notes:

1. Roman numbering

	MS.NET has "Oxford style" which for example converts 99 as
	XXXXXXXXXIX. It is not violating XSLT 1.0 spec. However, section
	7.7.1 explicitly describes 4 and 9 as iv and ix, so the "strict"
	Oxford style violates the spec.

2. Name conflict in variables

	If there is a conflict between a template local variable and a
	for-each local variable, MS.NET raises an error. It is a spec bug
	that does not define the behavior (like "implementation MAY reort
	an error ..., or recover ...).

3. Indentation behavior difference 

	Even if the xsl:output method is "xml", when indent="yes" is
	specified, the indentation behavior is different depending on the
	passed Transform() outout argument; TextWriter, or XmlTextWriter.

	Currently many of ConflictResolution tests comparison give us
	different results. We always use XmlTextWriter (which should be sane
	for <xsl:output method="xml" />), but with XmlTextWriter:

		XmlTextWriter w = new XmlTextWriter (Console.Out);
		w.Formatting = Formatting.Indented;
		w.WriteString ("- ");
		w.WriteStartElement ("Foo");
		w.WriteEndElement ();

	gives

		1: - 
		2: <Foo />

	on both MS.NET and Mono, unlike those ConflictResolution tests expect:

		1: - <Foo />

	So Microsft must have another writer for XML output, but I don't
	think that makes sense (at least it brings inconsistent indentation
	behavior).

4. namedtemplate_namedtemplate06

	The stylesheet must be rejected due to the restriction described in
	the spec 5.7. OASIS test suite currently contains REF_OUT but there
	should be no reference output.