> 1. The described result can be valid if there are "doubly quoted" strings in the input list.

To check this I've modified your testcase.py:

diff --git a/testcase.py b/testcase.py
index b597205..fefcef2 100755
--- a/testcase.py
+++ b/testcase.py
@@ -53,6 +53,11 @@ for entry in input_list:
 	# Conveting
 	conv_entry=urllib.parse.unquote(entry)
 
+	if conv_entry in bad_boys:
+		flag=True
+		print("ABOUT TO APPEND A BAD BOY")
+		print("Conversion:",entry,id(entry),end=" ")
+
 	# Printing (debug)
 	if flag:
 		print(">>",conv_entry,id(conv_entry))
@@ -61,7 +66,7 @@ for entry in input_list:
 	output_list.append(conv_entry)
 
 	# Printing (debug)
-	if entry in bad_boys:
+	if flag:
 		print("Just appended:", output_list[-1], id(output_list[-1]))
 		flag=False	
 		for x in output_list:

Let's run it and look for my new message:

$ ./testcase.py | fgrep -A1 -e ABOUT
ABOUT TO APPEND A BAD BOY
Conversion: eil%252fx2_firmware 139920242273280 >> eil%2fx2_firmware 139920244465360
--
ABOUT TO APPEND A BAD BOY
Conversion: seil%252fb1_firmware 139920242325448 >> seil%2fb1_firmware 139920241899608
--
ABOUT TO APPEND A BAD BOY
Conversion: seil%252fx1_firmware 139920242325520 >> seil%2fx1_firmware 139920241899752
--
ABOUT TO APPEND A BAD BOY
Conversion: seil%252fx2_firmware 139920242325592 >> seil%2fx2_firmware 139920241899896
--
ABOUT TO APPEND A BAD BOY
Conversion: seil%252fx86_firmware 139920242356704 >> seil%2fx86_firmware 139920241901408
--
ABOUT TO APPEND A BAD BOY
Conversion: seil%252fturbo_firmware 139920242416280 >> seil%2fturbo_firmware 139920242993744
--
ABOUT TO APPEND A BAD BOY
Conversion: seil%252fneu_2fe_plus_firmware 139920242065856 >> seil%2fneu_2fe_plus_firmware 139920243007536
--
ABOUT TO APPEND A BAD BOY
Conversion: intelligent_platforms_proficy_hmi%252fscada_cimplicity 139920241710560 >> intelligent_platforms_proficy_hmi%2fscada_cimplicity 139920244342480
$ fgrep -ne 'seil%252fneu_2fe_plus_firmware' data.txt
15191:seil%252fneu_2fe_plus_firmware
$ 

So, there is indeed a "doubly" quoted data, at 15191 in data.txt.

This is not a bug, everything work correctly.

This issue needs to be closed.