The primary issues affecting Signal, WhatsApp, Telegram, ProtonMail, and Tutanota generally revolve around a mix of privacy design limitations, metadata collection, government pressure, and occasional service outages or functional bugs.

Here's a breakdown of the key issues for each service:

Signal
Signal is widely regarded as the most privacy-focused, but it still faces some inherent challenges:

Phone Number Requirement: Signal requires a phone number for registration, which links the account to a real-world identity. While attempts are made to obfuscate this, it's a major point of metadata collection.

Metadata: Although Signal encrypts message content, it still collects some metadata about who is communicating with whom and when.

WhatsApp
As a service owned by Meta (formerly Facebook), its issues are primarily centered on corporate policy and data collection:

Parent Company Trust: The single biggest issue is a general lack of trust in its parent company, Meta, due to its business model of data collection and targeted advertising.

Centralized Backups: While chats are end-to-end encrypted, the optional cloud backups (e.g., to Google Drive or iCloud) are often not encrypted by default or the encryption keys are managed by the cloud provider, creating a potential vulnerability.

Metadata Collection: WhatsApp collects significant metadata about users, including contacts, usage data, and device information, which is shared with Meta.

Business Messaging: Chats with businesses that utilize certain optional Meta services (e.g., for storage or AI assistance) are not considered end-to-end encrypted by default after they are received by the business, which can be confusing for users.

Telegram
Telegram's main issues stem from its unique encryption implementation:

Non-Default End-to-End Encryption (E2EE): The major security issue is that E2EE is not enabled by default for all chats. Only Secret Chats and voice calls are E2EE. Standard cloud chats are encrypted, but Telegram holds the keys, meaning the company could technically access the messages.

Custom Encryption Protocol (MTProto): Telegram uses its own custom-built encryption protocol, MTProto, which has faced scrutiny and criticism from some cryptographers who generally prefer protocols that have undergone more rigorous, widespread peer-review (like the Signal Protocol).

Content Moderation/Abuse: Due to its massive channels and groups, Telegram frequently faces issues related to moderation, spam, and the spread of illegal or extremist content.

Service Reliability: Like any centralized service, it can experience occasional connection or messaging outages.

ProtonMail & Tutanota (Tuta)
These are end-to-end encrypted email services that share some challenges related to search and interoperability:

Limited Interoperability: Encrypted email only works seamlessly if both the sender and receiver use the same service (e.g., ProtonMail to ProtonMail) or if the sender uses a mechanism like password-protected messages for external recipients. Messages sent to regular email providers are not E2EE.

Search Limitations: Due to E2EE, the full content of your inbox is encrypted, which means the services cannot perform server-side searches, leading to slower or more restricted client-side search functionality compared to services like Gmail.

Tutanota (Tuta) Specific: The company has reported a significant issue with its visibility in Google search results for non-branded keywords like "secure email," which it alleges is harming its business.

ProtonMail Specific: Users occasionally experience minor issues related to login, mobile app stability, or integration with third-party mail clients (which requires a special 'Bridge' application).

Common Issues Across Encrypted Apps
Beyond individual platform issues, the wider ecosystem faces general challenges:

Government Pressure: All secure communication providers are under increasing pressure from governments worldwide (e.g., in the EU, US, and UK) to potentially add "backdoors" or comply with surveillance requests, which could compromise their security model.

Malware/Device Vulnerabilities: The encryption is only as strong as the endpoint devices. If a user's phone or computer is compromised by malware or a vulnerability, an attacker can access the messages after they've been decrypted on the device.

Usability vs. Security Trade-offs: Features that enhance security (like complex key verification) can often be difficult for the average user to understand or implement, leading to user error or neglect of key security steps.